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WARNING: MAJOR SPOILERS AHEAD
Pilot/Episodes 1 and 2: Independence Day and Fireworks
Takes place during July 4
Teenage superheroes Robin, Speedy, Kid Flash and Aqualad - Sidekicks, respectively, to Batman, Green Arrow, The Flash and Aquaman - are taken to the Justice League's headquarters for the first time, but are disappointed that they will only have limited access (read: only slightly better access than the public). Speedy storms off after a rant about how disrespectfully the elder heroes have treated the younger. The League then receives a report about a fire at Project Cadmus, a suspicious research project, but get called away to deal with another crisis. The kids decide to investigate Cadmus on their own. They find out that Cadmus has been secretly creating living weapons called "genomorphs", including a clone of Superman named Superboy. They try to rescue him, but he turns on them and captures them.
The project's director, Dr. Desmond, is told by Cadmus' board of directors to dispose of the young heroes and replace them with clones. However, Aqualad manages to help Superboy break his Mind Control and he helps them escape. It is then revealed that the genomorphs' leader, Dubbilex, had secretly helped the heroes as he wanted them to help his brethren. Desmond tries to stop them by drinking a genomorphic chemical that turns him into a superstrong monster form. Still, the young heroes defeat him by working together. The League then shows up, and lectures the kids for acting on their own, but they stand up to them and convince them to allow them to be a team, although an undercover one. The Martian Manhunter's niece, Miss Martian, joins the team in the end.
- The Cadmus Project is based on the DNA Project, a concept created by Jack Kirby for DC Comics in the 1970's, including the characters of The Guardian and Dubbilex. The DNA Project became Project Cadmus after the Crisis on Infinite Earths, and was later responsible for Superboy's creation.
- The name of the project that the serum used by Dr. Desmond to transform was codenamed Blockbuster, an homage to the codename his comic book counterpart used (a DC Comics Captain Ersatz of The Incredible Hulk).
Episode 3: Welcome to Happy Harbor
Takes place during: July 5 - 8
The Cold Open has the team (sans Superboy and Miss Martian) teaming up with Speedy against a superstrong criminal. They win, and the kids ask Speedy to join the team, but he rejects them. They return to "the secret mountain base thing" (Mount Justice, the League's old headquarters, where they are now based). Superboy angsts, and Miss Martian tries to commiserate with him telepathically; however this just makes him mad. Robin explains that people on Earth don't like having their minds read, and that it probably reminds Superboy of the mind control he was under. Their team mentor, Red Tornado, then arrives. Miss Martian tries to read his mind but cannot, because he's a robot. Later the team goes on a joy ride in Miss Martian's alien spaceship. Red Tornado contacts them to tell them about an attack on Happy Harbor, the town near their base.
The villain, Mister Twister, defeats the team easily. Due to being unable to read his mind, Miss Martian incorrectly deduces that he must be Red Tornado testing them. Superboy gets angry at Miss Martian for 'tricking' them into thinking Mister Twister was Red Tornado. Twister attacks somewhere else, seeking to fight Red Tornado. Miss Martian comes up with a plan and tells the team via telepathy.
Red Tornado shows up and takes on Twister by himself; he seems to be defeated. Mister Twister tries to reprogram Red Tornado. Surprise! It's actually Miss Martian in disguise (she can change form at will). Mister Twister is defeated by the kids using real teamwork. His chest opens up to reveal a scrawny guy inside, meaning Twister was really a robotic suit. Miss Martian smashes the pilot with a giant rock. The team is suitably outraged until she reveals that he was actually a robot (which makes it totally okay to destroy it) which she could tell since she couldn't read his mind either.
They take the broken remains of the scrawny robot back to Mount Justice. Red Tornado suspects it may have been after him. The scene cuts to a guy (who is revealed to have been piloting Mister Twister remotely) and his boss. At the end of the episode, Superboy finally apologizes to Miss Martian, leaving them on a good note.
- In the original comics, the Justice League abandoned their original headquarters for the Justice League Satellite after its secret was compromised (as said this episode); the person who betrayed them was their own teenage team mascot, Snapper Carr. Note also that there was no interim Hall of Justice headquarters (The Hall was invented for the Superfriends animated television show; it was added in the comics later).
- The unnamed Scary Black Man in the Cold Open is Brick, a minor enemy of Green Arrow.
- Mister Twister is based on an obscure Teen Titans villain--in fact, the very first one. Robin, Kid Flash and Aqualad formed the Teen Titans after defeating Twister.
- The scientist in the end seems to be T.O. Morrow, the villain who created Red Tornado.
Episode 4: Drop Zone
Takes place during: July 19 - 23
They discover that Kobra is turning the Venom drug into a Super Strength-granting serum (using the Blockbuster formula from episode 2) for a special client - The Sportsmaster. However, the kids accidentally reveal their presence and decide to deal with the situation by themselves. This leads to a conflict over leadership that has Robin pass it over to Aqualad. The kids have to join forces with Bane, who betrays them in the end (but they deal with him). Kobra escapes when faced by the whole team. The Venom factory is destroyed, and Sportsmaster escapes with a sample for his masters, The Light, who decide that the teen heroes are interfering too much.
- Kobra was a villain with his own series, created by Jack Kirby in the 1970s, and his group is not based on the G.I. Joe characters (though it still might be a tribute when they chant his name.)
Episode 5: Schooled
Takes place during: August 3 - 4
The superheroine Black Canary begins training the kids in combat, but is rejected by Superboy, who is already irritated that Superman refuses to acknowledge any relationship to him.
After the League defeats Amazo, an android that duplicated all of their powers, they dismantle it and ship the remains off to a laboratory to be studied. The Team is charged with watching over the transport convoys. However, Amazo's creator, Professor Ivo, manages to recover its parts (due in part to Superboy's overconfidence) and reassembles the android. Superboy tries to fight it, but gets a beating, even with Robin and Kid Flash's help, until they outsmart him by threatening its creator, confusing it to the point that it telefrags itself onto Superboy's fist. Even though Dr. Ivo escapes, Batman congratulates the team on a job well done.
There is also a scene in the episode featuring Bruce and Clark having a short meeting in a diner to discuss Superboy, when Batman suggests that in a way, Superboy is Superman's son, Clark storms out angrily.
In the end, Amazo is disassembled again, and Superboy accepts Canary's mentorship.
- The flying robot monkeys are obviously a The Wizard of Oz reference.
- The fight against Amazo takes place in Robin's school, apparently by accident.
- An arrow shot by an unseen person helps during the battle; while Robin, Kid Flash, and Aqualad assume this to be Speedy's handiwork, it's actually the first action by Artemis in the series.
Episode 6: Infiltrator
Takes place during: August 7 - 9
A criminal organization called The League of Shadows kidnaps a scientist and forces her to create a weapon for them, a cloud of nanites that not only consumes matter but can also steal data from computer systems. Speedy, now calling himself Red Arrow, rescues her but not before they get the weapon.
Red Arrow goes to The Team to ask for help in keeping the inventor safe from The League while she finishes creating a computer virus that can nullify the cloud. He finds out that Green Arrow now has a new sidekick, his niece Artemis, who has just joined the team, and he is not pleased. Her attitude rubs the team wrong as well.
The League sends the assassin Cheshire and two other villains (Black Spider and Hook) to kill the scientist, and the team fails to stop her, but she spares her target once she finds out that the virus has already been finished. Artemis almost captures Cheshire, but then lets her go when she threatens to reveal some facts about Artemis' past to the team.
In the end, Red Arrow tells Artemis that he knows she's not really Green Arrow's niece (probably because GA raised him), but he won't tell the others, unless she does something to hurt his friends.
Also, The League is seen to work for The Light, and they state that they now have an agent inside the team.
- In the comics, Cheshire seduced Speedy and had a daughter with him, whom he raised on his own (until she was killed off for shock value.)
Episode 7: Denial
Takes place during: August 19 - 20
Kent Nelson, once the mystic hero Doctor Fate, is captured by Abra Kadabra (a supervillain who pretends to be a sorcerer) for Klarion the Witch Boy (who is a real sorcerer), so they can find the former source of his powers, the Helmet of Fate.
Red Tornado sends The Team to investigate Nelson's disappearance. Wally (Kid Flash), who doesn't believe in magic, pretends to do so just to get on Miss Martian's good side. But this causes problems when they try to enter Fate's Tower and its mystical defenses detect the lie.
Later on, Wally helps Nelson reach the helmet, but Klarion kills the old man. Wally then puts on the Helmet of Fate and it takes over him, turning him into Doctor Fate, who defeats Klarion by striking at his Familiar, a cat. Nelson's spirit then convinces Nabu (the spirit inside the helmet) to let Wally's body go free.
Wally takes the Helmet to Mount Justice for safekeeping, and doesn't tell the team the full story of his possession (and insists he still doesn't believe in magic.)
- Madame Xanadu, the fake seer in the episode's opening, IS a real sorceress in DC Comics - Merlin's former lover Nimue, in fact.
- Similiarly, Klarion is not a Lord of Chaos in the comics.
- Robin is absent from this episode, supposedly out on a mission with Batman. This was expanded on in issue #11 of the tie-in comic.
Edisode 8: Downtime
Takes place during: August 27 - September 3
After Batman points out that he is performing poorly as leader due to homesickness, Aqualad returns to Atlantis to decide if he should stay there. He hopes to declare his love to his childhood friend Tula, only to find out that she has fallen in love with his old friend, Garth. Meanwhile, the forces of Black Manta attempt to steal a frozen creature from Atlantis, only to be foiled by Aqualad and Garth.
In the end, Aqualad decides to return to the surface world, while Manta reports to his employers, The Light.
- The team does not work together this episode; the others are shown spending time with their loved ones (or, in Miss Martian and Superboy's case, hanging around Mount Justice).
- In the comics, Garth was the first Aqualad, and Tula was his girlfriend; she was killed long before ever meeting the second. Later, Garth assumed the identity of the magic-using Tempest.
- In fact, when he uses magic, if you listen to the words you can hear him use the word "tempest" in his spells.
- Mera is revealed to be pregnant this episode; in the comics, Manta killed her and Aquaman's infant son.
- In the comics, Black Manta has another relation to Aqualad: he's his father. Time will tell whether the show will use this plot point or not. (Word of God confirmation that this relationship exists suggests they might)
- Artemis' name in this episode is revealed to be Artemis Crock. In the comics, Artemis Crock is an archer whose father is the Sportsmaster. Make of that what you will.
- In the comics, Topo is a normal octopus, rather than an humanoid one.
- There's a version of the humanoid Topo in the Aquaman series with his temp replacement Arthur Joseph Curry.
- The frozen creature in this episode, with its resemblance to a giant starfish, is most likely Starro the Conqueror, though apparently unknown yet in this continuity.
Episode 9: Bereft
Takes place during: September 3 - 4
Miss Martian stumbles through a desert at night, at first not even realizing she's on Earth. Superboy crashes next to her and acts feral, neither recognizing each other. Robin wakes up and learns they're in Bialya, having no idea how he got there and realizing there is a six-month gap in his memory. Finally, Kid Flash and Artemis wake up in a shack, also having fractured memories. Eventually, Miss Martian is able to repair their memories using her telepathy, getting Robin, Artemis, Kid Flash and herself back to normal as well as finding Aqualad, who is badly dehydrated. Superboy, however, has been captured by Psimon and Bialyan troops who are testing some new technology on him. Miss Martian goes for the rescue and ends up in a psionic duel with Psimon, who made them lose their memories in the first place. Superboy, after some help from the extraterrestrial sphere that the team was sent to the country to examine, gets his memories back and helps Miss Martian take Psimon down. The team escapes with the sphere in tow, Aqualad finally coming to.
Psimon reports to the Light, who show footage of the sphere's arrival via boom-tube (the preferred mode of transportation for people like Darkseid and the New Gods) and remark that more will be coming.
- Artemis suggests, after seeing the bow and not having her memory back, that she's there with Kid Flash to kill him as a part of one of her dad's tests. Later after their memories are restored, Artemis denies it being reality, claiming she was just confused by a TV show she saw. This suggests that she is possibly Sportsmaster's daughter as hinted last episode.
- The alien sphere appears to be some variant of a Mother Box, which is technology from New Genesis.
- One of the voices of the Light was Marina Sirtis, who will supposedly be voicing Queen Bee.
Episode 10: Targets
Takes place during: September 7 - 8
Peace talks between North and South Rhelasia (Expies for North and South Korea) break down, and an unidentified mediator is called in. Red Arrow is at the talks in his civilian clothes, presumably to ensure no interference from any outside organizations. Just as the mediator shows up, Cheshire attacks, but Red Arrow, along with the present security forces, manages to take her down. Cut to a stunned Red Arrow (and the media, for that matter) when the mediator turns out to be... Lex Luthor.
Lex assures Red Arrow that he believes peace will give him a shot at increased profits, then hires him to help him ensure the peace talks go smoothly, although Red Arrow refuses the money. Heading to Cheshire's holding cell to interrogate her, Red Arrow witnesses her breakout by Sportsmaster. Tracking them, Red Arrow arrives to find out their boss is none other than Ra's Al Ghul.
Calling in Aqualad for backup, the pair investigate further and manage to stave off the combined efforts of Sportsmaster and Cheshire; however, Lex Luthor saves the day for his cameras when his secretary turns out to be an advanced combat android which shoots down Sportsmaster, which he quickly capitalizes on. Enthralled by the new technology, the two Rhelasias sign an accord under the auspices of Luthor. Annoyed by this turn of events, but happy the situation was resolved peacefully between the two parties, Red Arrow and Aqualad depart for their respective bases - but only after Red Arrow privately admits his respect for Aqualad and his team.
At the very end, Lex Luthor is seen talking to someone about the deal... the camera pans out to reveal Ra's as his partner in crime.
Miss Martian and Superboy attend the first day of school. Miss Martian tries out for the cheerleading squad.
- Artemis, Kid Flash and Robin are not seen in this episode.
- Miss Martian and Superboy are not privy to the civilian identity of Superman, Clark Kent. When Martian Manhunter suggests "Kent" as a last name for Superboy, they believe it to be a reference to Dr. Fate, Kent Nelson, whom they have previously met.
- Several minor DC characters including Wendy and Marvin from the Superfriends cartoon, Mal Duncan and Karen Beecher from the Teen Titans, and Snapper Carr are seen.
- Rhelasia was created by Chuck Dixon for the first Birds of Prey one shot.
Episode 11: Terrors
Takes place in September 14
The League captures the Terror Twins, a Brother-Sister Team of supervillains. However, it is a disguised Superboy and Miss Martian who get sent to prison in their stead.
It turns out that Batman suspects that the various ice-powered villains (all captured in the first episode) are getting themselves arrested on purpose, to be transported to Belle Reve, a prison for supervillains, and he wants to know why. While the two young heroes infiltrate it, Aqualad and Red Tornado watch from an invisible airship nearby. The prison is under the control of Amanda Waller, the warden, and the psychologist Dr. Hugo Strange.
In the prison, everyone wears collars that inhibit their powers and can be used to shock them into submission. This includes the heroes; only Miss Martian's telepathy still works.
Superboy 'befriends' Icicle Jr., a young villain whose father, the original Icicle, is the "prison boss". It turns out the villains were waiting to use their combined supercold powers to make the prison walls brittle enough to smash through. They manage to free all the prisoners. However, Superboy tricks Icicle Jr. into helping him reactivate the prisoners' collars.
In the end, Waller is fired and replaced with Strange - which was Icicle Sr.'s goal all along; they both work for The Light. Out of all the criminals, Edward Nigma, aka The Riddler, somehow managed to escape.
- The prison, Waller, and the concept of the inhibitor collars are all based on the DC Comics series Suicide Squad.
- Hugo Strange is an old Batman villain.
- Superboy and Miss Martian kiss for the first time.
- Second episode in a row where Kid Flash, Artemis and Robin do not appear, and Robin's third overall. If we count the episodes prior to her formal introduction, this is Artemis' seventh non-appearance; otherwise, it's her and Wally's second.
Episode 12: Home Front
Takes place in September 22.
Artemis attends her first day of school in Gotham. When she and Robin return to the Cave, they find themselves under immediate attack. Kid Flash, Superboy, Aqualad and Miss Martian have been captured and are held hostage; the two badass normals hide in the headquarters but are given ten minutes by the supervillains to give themselves up or their friends will die.
- The antagonists are not named on screen, but they are Red Torpedo and Red Inferno, two androids similar to Red Tornado (he doesn't know about them though.)
- This episode verifies the fan theory that Artemis and Cheshire are related (they're sisters.)
- This episode has cameo appearances by Bette Kane and Barbara Gordon, the first two incarnations of Batgirl, who attend high school alongside Artemis and Robin. Neither is shown to have a costumed identity.
- Robin appears to have figured out Artemis' secret identity, but she doesn't recognize him.
Episode 13: Alpha Male
Takes place September 23
The Brain and Monsieur Mallah are enslaving animals in a jungle, and Batman sends the team (which after Red Tornado's disappearance will now have a rotating Justice League mentor, beginning with Captain Marvel) to investigate, but Superboy overhears that Aqualad knew about The Mole, and this causes friction within the team.
- The tiger in this episode is an homage to Mister Tawky Tawny, an humanoid tiger that used to be a funny sidekick to Captain Marvel.
- Superboy gets another pet, a wolf he names Wolf.
Episode 14: Revelation
Takes place October 1
The Injustice League holds the world hostage with giant monster plants. While the Justice League deals with them, the young heroes are sent to find the enemy base.
In the end, the whole thing turned out to be yet another plan of The Light, to clue the heroes away from their existence.
- The members of the Injustice League are Count Vertigo, Wotan, Black Adam, Atomic Skull, Ultra-Humanite, The Joker and Poison Ivy.
- Their headquarters turned out to be the same one used by the Legion of Doom in Challenge of the Superfriends.
- The members of The Light are fully revealed: They are Lex Luthor, Ra's Al Ghul, Vandal Savage, Queen Bee, Ocean Master, The Brain and Klarion The Witch Boy.
- Aqualad dons the Helmet of Doctor Fate to battle Wotan. He doesn't stay possessed by it though.
- The episode features cameos by several heroes not yet seen in the show including Blue Devil, Plastic Man, Rocket and Icon.
Episode 15: Humanity
Takes place October 10
T.O. Morrow holds Red Tornado captive and creates a new android, Red Volcano, with his memories so he can defeat the Justice League. But Volcano decides instead to destroy the human race! With help from Zatara's daughter Zatanna, the team finds the androids, though it is ultimately Red Torpedo and Red Inferno who stop Volcano, making a Heroic Sacrifice.
- Zatanna is a teenager in this version.
- Morrow is revealed to be a very old, dying man, unlike in the comics; the younger one we see is an android.
- Both Red Torpedo and Red Inferno (as Firebrand) are based on old DC comics superheroes (neither one was an android however.)
Episode 16: Failsafe
Takes place on October 16
When an army of aliens attack Earth, things go from bad to worse. First, the entire Justice League (minus Martian Manhunter) is killed by alien weapons which can cut through seemingly anything. Then, when the team manages to steal one of those weapons and integrate it into Miss Martian's bioship, Artemis, Aqualad, and Wolf are killed. When the team recruits all the recurring heroes that they could think of (Red Arrow, Zatanna, Icon, Garth, and Tula), an alien mothership lands in (and totally destroys) Smallville. The team manages to get inside the mothership and destroy it, but only with the lives of Kid Flash, Robin, and Superboy, leaving just Miss Martian and Martian Manhunter alive. As they look at the mushroom cloud that used to be the alien mothership, another swoops down out of the sky. Martian Manhunter, who has been trying to remember something throughout the episode, finally remembers what it was, and stabs Miss Martian through the chest.
In the end, it was all a training exercise Gone Horribly Wrong. While the team knew going in that it was a training exercise in a virtual reality, they did not know two critical pieces of information. First, the simulation was completely unwinnable, as the scenario would make things worse no matter what the team did. Second, Miss Martian's subconscious couldn't accept that it was just a simulation when Artemis died and thus changed the rules so that Your Mind Makes It Real. Martian Manhunter figured out only way to break out of it was to shock Miss Martian back into reality, but explained afterwards to Batman and Red Tornado that her telepathic powers, though untrained, were extremely dangerous and far more powerful than his.
- The general that greets the teens when they arrive at the Hall of Justice is Wade Eiling, a character created by Greg Weisman for his run on Captain Atom in the 1980s. In issue #9 of the Young Justice tie-in comic, which takes place between the episodes "Infiltrator" and "Denial," Captain Atom sends the team to investigate a cold murder case as part of their covert ops training. Eiling is posited as the one most likely to have framed the person previously convicted of the crime--so the kids would have already heard of him before the episode.
Episode 17: Disordered
Takes place on October 23
In the wake of the team's last mission, Black Canary plays counselor to the team members, helping them get through the depressed feelings each of them are feeling. Superboy walks out on the counseling early, taking the Sphere with him. While out, he meets The Forever People, of the good New Gods- it turns out Sphere is actually their sentient vehicle, the Super Cycle. Superboy joins the team to recover other technology from their world on Earth, and they discover a scheme by Darkseid's minion, Desaad, to steal the Infinity Man, the Forever People's combined self, for himself.
- The Infinity Man is treated almost like a Humongous Mecha, rather than a Cosmic Entity as in the comics.
- In the comics, Infinity Man was not a gestalt of the Forever People; he just traded places with them.
- Superboy gets to keep the Super Cycle, which is the team's mode of transportation in the original Young Justice comics.
Episode 18: Secrets
Takes place on October 31
Harm, a psycho who stole the magic sword of Beowulf, stalks Artemis and Zatanna as they go on patrol. They are assisted by a mysterious girl who only says the word "Secret". Meanwhile, the rest of the team goes to a Halloween party at their school, where Marvin tries to prank them by claiming Martians are invading. Miss Martian is not amused.
- The "Abel's House of Secrets" sign is a Shout-Out to House of Secrets, an old DC comics title. The host Abel later turned up in The Sandman with his brother Cain, who in turn hosted House of Mystery.
- As part of a Halloween prank Miss Martian shapeshifts into a form reminiscent of Marvin the Martian. Like the DC Comic universes, Looney Tunes is another WB animated franchise.
- This episode confirms that Robin is already aware of Artemis' real identity.
- At the Halloween party, Mal is dressed up as 90s Superboy, calling it "Superman, done right". Also, Karen's costume is Bumblebee, who was the main inspiration for her character.
- Wally's costume is either a nod to Teen Wolf or I Was a Teenage Werewolf. Megan's looks like Corpse Bride.
- Secret and the episode's new villain Harm first appeared in the Young Justice comic series.
- Harm uses the Sword of Beowulf. While the depiction of the sword is unique to the show, Beowulf actually exists in the DC Universe; he had an eponymous comic in the 70s, and in recent years has appeared in Wonder Woman.
Episode 19: Misplaced
Takes place November 5 to 7
Klarion the Witch Boy, with the help of four other sorcerers, casts a spell that splits the world in two, one for adults and one for everyone under 18. Each half of the population thinks the other has vanished.
Captain Marvel discovers the truth when he switches to his adult form and is whisked to the "adults' world." He helps the Justice League get in touch with the Young Justice team, and together they attack the four sorcerers and Klarion (respectively.) Zatanna is forced to put on the Helmet of Fate to fight Klarion, who escapes.
After the Earths remerge, Fate refuses to release Zatanna saying his presence is needed, until her father, Zatara, agrees to be his host instead.
In the end, the effectively orphaned Zatanna stays with the team at their Mountain Headquarters. We also see that the whole deal was a distraction so other members of The Light could recover a piece of Starro The Conqueror from S.T.A.R. Labs.
- This episode is based on the story "World Without Grown-Ups" that (in the comics) led to the formation of Young Justice in the first place.
- The sorcerers helping Klarion are: Felix Faust, Blackbriar Thorn, Wotan and The Wizard, enemies of (respectively) The Justice League, Etrigan, The Spectre and the Justice Society.
- Cameo appearances in this episode include Commissioner Gordon, Barbara Gordon, Bette Kane, and Rocket.
- Zatara's fate sidesteps the Cruel and Unusual Death he got in the comics.
- Klarion went to Roanoke Island to start his spell which, in Grant Morrison's Seven Soldiers, is tied to where Klarion grew up since his home of Limbo Town was based on "The Lost Colony" that had once tried to settle in Roanoke Island but mysteriously disappeared.
Episode 20: Coldhearted
Takes place November 11 to 13
When mysterious machines cause a snowstorm across the United States, the team must work with their Justice League mentors to stop them. Except Kid Flash, who is given the mission of delivering a human heart for an urgent transplant. He's annoyed at missing the team-up, until he finds out that some supervillains want to prevent the transplant for some reason. ( The girl being operated is the rightful queen of Vlatava, an European country, and her evil uncle Count Vertigo wants the throne.)
- We learn that November 11 is Kid Flash's birthday.
- Where and how Vertigo got the snow machines is left a mystery.
- Key characters in the episode appear in the DC Showcase: Green Arrow short film, and the same voice actors reprise their roles.
Episode 21: Image
Takes place November 22 to 23
The leader of the Nation called Qurac, situated next to the dictator-run Bialya, has just announced plans to "reunite" the two countries under the evil Queen Bee's rule. Suspecting mind-control, Batman has the team (minus Artemis, Zatanna and Aqualad) go in to investigate. The plan goes awry, though, when they're forced to save a young boy and his mother, the latter of whom Megan seems to know and idolize. This is because she's a former actress who played the character of Megan on a TV show, on whom she based her current form. M'gann is then mind-raped by Psimon, who discovers her true form and forces her to face her greatest fear - that the others will reject her if they ever discover it.
- The Hello, Megan! TV show is finally shown directly after some hints or teases in previous episodes.
- Miss Martian's identity as a White Martian is confirmed.
- It is implied that Beast Boy will gain his powers through a blood transfusion from Miss Martian.
- The TV actors have counterparts (or at least namesakes) in the comics, where they really were actors before taking up costumed identities. One example is Rita Farr, the superhero Elasti-Girl of the Doom Patrol. The exception is the original Megan herself, but she's the mother of the future Beast Boy.
Episode 22: Agendas
Takes place on November 25.
Superboy receives a message from Lex Luthor, who is now in charge of Project Cadmus. He suspects that a second clone of Superman has been created by the project, and Superboy reluctantly goes back to Cadmus to investigate. Though Guardian assures him that no such clone has been created, Superboy discovers another clone in a capsule, labeled "Project Match". This clone proceeds to violently attack Superboy, knocking him out and escaping. After recovering, Luthor informs Superboy that he is in fact half-human, and that the other clone's full-Kryptonian DNA has driven it insane. Dubbilex, the lead genomorph from the pilot episode, guides Superboy to 'Genomorph City', an underground area where the genomorphs have been escaping to so that they could lead their own lives. The clone is there as well and Superboy uses a special patch Luthor gave to him to unlock more of his Kryptonian powers temporarily. After the clone is subdued, Superboy confronts Luthor directly about the incident, where Luthor reveals that he was the donor of Superboy's human DNA; Superboy attempts to attack Luthor over this news, but is subdued by the phrase "Red Sun/Son", leaving him alone some time later.
Meanwhile, the Justice League has been debating whether or not to induct new members into the league, as well as questioning the presence of Dr. Fate and Captain Marvel on the team. The episode ends with the League ratifying their decision regarding new members, though what that decision is was not revealed before the end of the episode.
- Wonder Woman makes her first voiced appearance in the show, voiced by Maggie Q.
- Superboy is confirmed to be a half-human clone of Superman, with the human DNA coming from Lex Luthor, much like in the comics.
- Superboy's "clone brother" (called Match) featured in this episode is from the comics as well, though his background and appearance are different there. In the show, he is actually the first attempted clone of Superman; Superboy was created after the pure-Kryptonian DNA drove it insane.
- Guardian is revealed to be Roy Harper/Red Arrow's uncle, again like in the comics.
- Luthor's frequency line references Superman the Movie.
Episode 23: Insecurity
Takes place on December 4-5.
Half the team is sent to track down Sportsmaster, who is making a special delivery (the piece of Starro The Conqueror stolen in "Misplaced") to a group of villains. He's being assisted by Cheshire, and this causes Artemis to go after her rather than focus on the mission. Red arrow (who has joined the team to look for The Mole within it) suspects her of being a traitor.
Meanwhile the other half sneaks into Red Tornado's room to find out what he does there, and discover that he's building an human-looking body for himself.
- The Spider-Man-like villain seen at the beginning is Black Spider, an enemy of Batman. This is an in-joke since Young Justice writer Greg Weisman also worked on The Spectacular Spider Man. Black Spider is also voiced by Josh Keaton, who also voiced Spidey in said series.
- The blonde girl in the beginning is Cissie King-Jones, better known as Arrowette in the original Young Justice comics.
- Artemis' parents are finally revealed to be Sportmaster and the (villainous) Huntress, just as in the comics. (Batman and Green Arrow are aware of this.)
- Red Arrow was admitted into the Justice League, but is asked by Green Arrow to join the YJ team first.
Episode 24: Performance
Takes place on December 22-24.
According to Robin, Batman has sent him, M'gann, Artemis and Superboy to investigate a series of robberies coinciding with the movements of a circus tour. Red Arrow, who is still suspicious of there being a mole, joins. The group joins the circus as the Daring Danger family, a group of acrobats, but finds their attempts at tracking down both the culprit and blending in hindered by a flu going around.
It turns out that the villain is The Parasite, an enemy of Superman who saps the powers and abilities of others on touch, making them his own. His danger increases much more from the talents he'd been collecting from the circus performers to those of Superboy and Miss Martian.
- The circus they investigated was the one Dick Grayson (Robin) grew up in before his parents' deaths (they were a family of acrobats). In the end, the ringmaster recognizes him.
- The Hadron Supercollider figured in the villain's plan.
- Red Arrow concludes in the end that there is no mole in the team. Which is rather ironic, given the reveal in the next episode.
- Superboy continues to use the power-boosting patches Luthor gave him.
Episode 25: Usual Suspects
Takes place December 30
Several villains (including Cheshire) lay an ambush for Young Justice, but the heroes beat them with help from their new member, Rocket. They retrieve the suitcase lost previously, and find it filled of strange bio-tech chips which are clearly not from Earth. Later Luthor, Queen Bee and Sportsmaster summon Superboy, Miss Martian and Artemis to Santa Prisca. However none of them betray the team, and in fact they had all confessed their respective secrets to their teammates before going there. Of the three only Sportsmaster is captured.
Later we find out that the real mole was Red Arrow, who was an unknowing Manchurian Agent to Vandal Savage. The episode ends with the entire Justice League under his control.
- The Atom, Icon, Plastic Man and Red Arrow are all made members of the League. Dr Fate's membership also becomes official, inheriting Zatara's place on the team.
- YJ finds evidence that the supervillain prison, Belle Reve, is under criminal control.
- In this episode we discover that Cheshire still cares for her sister, and saves Artemis' life. Later she refuses to help her father evade capture.
- Its revealed that Superboy knew about M'gann's true Martian form since they shared a Battle in the Center of the Mind in Bialya, and was waiting for her to tell him the truth.
- Similarly, Robin reveals that he knew about Artemis's shady family for a while, since he's a master detective, and decided it didn't matter.
Episode 26: Auld Acquaintance
Takes place December 31
Vandal Savage and Klarion have the mind-controlled heroes of the Justice League pretend they are now free-willed again to trick Young Justice, but they figure this out and escape. With help from some allies, they manage to create a cure, and sneak into the League’s space headquarters where they must battle the possessed heroes to save them. They succeed, but Savage and Klarion escape.
- Red Arrow turns out to be a clone of the real Roy Harper (Speedy.) His mind control method was different from the others’.
- Superman finally acknowledges Superboy.
- The Cadmus labs are raided by The Light; among the things taken are Match and the (apparent) body of Roy, who is missing an arm.
- Some League members were missing for 16 hours, but don't remember what they did then.
Season 2: Invasion
Episode 1: Happy New Year!
Takes place January 1 to 4 (after a Time Skip of 5 years)
When Lobo publicly captures an alien disguised as the United Nations Secretary, a TV Talk show host begins spreading distrust of aliens, including the ones in the Justice League. With help from STAR labs scientist Adam Strange, the League discovers the places on Earth where the aliens are active, and send the Justice Squad (the teen heroes) to investigate. Blue Beetle, Robin (Tim Drake) and Lagoon Boy find their main base and rescue some hostages before it self-destructs.
- Zatanna and Rocket have joined the League. There are also three other members to have joined in that time, one of which is Black Lightning.
- Dick Grayson (Robin) is now Nightwing, and is now the leader of the team. Tim Drake has taken up the Robin mantle and joined them team. Batgirl is also now an active hero and member of the team.
- Other new members include Bumblebee, Blue Beetle, Mal Duncan, Lagoon Boy, Wonder Girl, and Garfield Logan as Beast Boy.
- Nightwing, Superboy, and Miss Martian have open invitations to join the Justice League, but they don't feel like it yet.
- Godfrey is an agent of Darkseid in the comics, in charge of manipulating the public.
- Adam Strange is not yet a space hero.
- The mission the mind-controlled Justice Leaguers can't remember (from the previous episode) was in the area of the planet Rann. Whatever they did was bad enough that there are arrest warrants for the entire League, not just the original six, in Rann space.
- Miss Martian and Superboy are no longer dating, and M'gann is now with Lagoon Boy.
- A comment by Captain Atom and some simple math indicates that only 21 Leagers are currently active, while the numbering scheme indicates that the roster has 26 members. Presumably Zatara would be one of the inactive ones but that leaves four others out of action.
Episode 2: Earthlings
Takes place January 5
Superboy, Miss Martian and Beast Boy arrive on the planet Rann with Adam Strange where they are helped by local scientist Sardath and his daughter Alanna in tracking down the Kroloteans who stole their zeta-beam teleportation technology. The heroes must sneak around since Earthlings are considered criminals there (because of what the mind-controlled League members did years ago.) They find the enemy base but are unable to prevent it from escaping (it was actually a disguised ship.)
- The Rannians do not speak English so they need to use Miss Martian's mind links to communicate.
- We find out that Superboy was the one who ended his relationship with Miss Martian. We don't know what happened, but he implies it was because of something she did.
- Superboy doesn't physically age. He says he's not immortal, he does age internally, but he'll always look the same as he does now.
- Queen Bee is responsible for the death of Beast Boy's mother, and that Beast Boy and Miss Martian are now adoptive siblings.
- Miss Martian mind rapes a Krolotean to find out what the Leaguers did (not revealed this episode.)
Episode 3: Alienated
Takes place January 5 to 26
Miss Martian returns to Earth and shares what she has learned. The Kroloteans try to build a spaceship to leave Earth (since the Zeta beam transport has been disabled) at a secret island base with help from Black Manta's son. The base is found and attacked by Batman, Aquaman, Superman, Wonder Woman and Martian Manhunter along with their respective sidekicks. Manta's son is revealed to be Aqualad, who is bitter that Aquagirl was killed and that Aquaman never told him who his actual father was. A Time Bomb (set by the Kroloteans' mysterious competitors) forces everyone to escape (except the Kroloteans, who die for refusing to believe Superman.)
In the end, the six Leaguers who attacked another planet while under The Light's control must leave Earth to face a trial. Black Manta officially joins The Light, filling the position left by Ocean-Master.
- Bibbo Bibbowski, the restaurant owner from the first part of the episode, is a minor character from Superman comics.
- It is revealed that the Justice League came together to repel an Appelaxian invasion. Several host bodies are currently on display in the publicly accessible portion of the Hall of Justice.
- Wonder Girl is revealed to have a mother, and may be living with her.
- Other exhibits include the armor of Guardian, a dismembered Amazo, and what appears to be Katana's katana.
- We see a growing embitterment towards the Justice League from the media.
- The Kroloteans' mysterious "Competitor" is implied to have a connection to Blue Beetle.
- Tula joined the Team as Aquagirl at some point during the 5-year gap, only to later be killed during a mission.
Episode 4: Salvage
Takes place February 12 to 14
Nightwing, Wally West (Kid Flash), Green Arrow, Black Canary, and Jim Harper (The Guardian) give Red Arrow, who is a wreck over his repeated failed attempts to find the real Speedy, a midnight rooftop intervention. Meanwhile Superboy and Blue Beetle track Intergang members who reanimate the Appellaxian Golems with Apokoliptian technology. They lose control of the combined creature, and it attempts to destroy a nuclear power plant in order to stop feeling pain. The Sportsmaster and an unseen ally (the same one working with Black Manta in the last episode) then destroy the Golem and mindwipe the two Intergang members.
- Wally and Artemis have retired from the superhero business and are attending the same college and still dating, as well as living together.
- Cheshire quit being a villain and married Roy, but returned to her former life when his obsession with finding the real Speedy took over everything else in his life. She just revealed to him that they have a daughter together, Lian Harper.
- Several components of Blue Beetle's history are presented in this episode. Jaime Reyes claims the Blue Beetle Scarab contains an AI that was invented by Ted Kord, the first Blue Beetle. It is implied Kord died before ever meeting Reyes, but that Superboy was familiar with his work. At several points in the episode it is shown the technology of the Scarab and Apokoliptian technology are "not compatible".
- According to Superboy the Justice League first fought the Appellaxians twelve years ago (six and a half years before the start of the series).
Episode 5: Beneath
Takes place February 18, 20
An all-girl team (composed of Wonder Girl, Batgirl, Miss Martian and Bumblebee) is sent to the nation of Bialya to investigate Queen Bee's new operation (since her mind control powers mostly work on men). Despite being found out, the heroines rescue some (but not all) of several teenage runaways, who had been kidnapped by the villains for unknown purposes.
One of the kidnapped teens was Tye Longshadow, a Native American friend of Jaime Reyes (Blue Beetle) who was looking for him, thinking he had been kidnapped by his mother's boyfriend. He's still a prisoner.
- Psimon has recovered from the coma Miss Martian put him in. He's still working for Bee.
- QB kidnapped the kids for an unknown villain, likely the same one who has been hinted at in previous episodes.
- The Longshadows are a reference to Apache Chief from the Superfriends show. Long Shadow was an Ultiman, based on Apache Chief, that appeared in Justice League Unlimited. Additionally, the other children still in captivity include an Asian, an African-American, and someone of indeterminate ethnicity. Smart money says he's Hispanic.
Episode 6: Bloodlines
Takes place February 28
A teenage speedster named Impulse arrives on Mount Justice from the future in a Time Machine, supposedly just to visit, and ends up confusing a lot of people. Impulse escapes Mount Justice and heads to Central City hoping to meet Barry Allen. Nightwing is able to contact both Barry Allen and Wally West about the imminent arrival of Impulse, but before Dick can finish Impulse rushes in on Barry and his wife Iris West celebrating Jay and Joan Garrick's 70th wedding anniversary.
Impulse reveals that he is the future grandson of Barry and Iris, and that Iris is pregnant with his Aunt Dawn and father. Iris West receives a call from her boss that a supervillian is attacking Central City. Mysterious beings manipulate this supervillain named Neutron into wrecking havoc in Central City. Both versions of The Flash (Jay and Barry), Kid Flash, and Impulse work together to stop Neutron. Impulse rushes in, and while the others aren't present, use a device to cure Neutron.
Elsewhere, Red Arrow and Cheshire, along with their daughter Lian, travel to a a Tibetan monetary in their search for the original Roy Harper. After fighting off an army of monastery guardians they finally locate Speedy and release him from stasis.
Having visited Barry, his original stated goal, Impulse climbs back into his time machine to return to the future. Nothing happens and it seems Impulse is now stuck in the present due to the machine's breakdown. We then flash-foward once again to the future Impulse came from, where it's implied originally Barry died that day and in time Neutron and others like him devastated the entire planet. Neutron himself was the one who built the capsule device that cured the villain in the past, and together with Impulse had planning all along to use the time machine to change the future for the better. Bart knew from the start that he would never be able to return home. Unfortunately, though Bart's actions save Neutron from 40 years of crime and destruction, the rest of the future is still in ruins.
- Barry Allen's grandson from the future, Impulse (Bart Allen), is introduced. He was one of the three founding members of Young Justice in the comics, together with Robin (Tim Drake) and Superboy.
- Jay Garrick, the original Flash, also appears this episode.
- The original Roy Harper is reintroduced after last being seen in "Auld Acquaintance".