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As he leads the Autobots further toward Earth's core, Megatron is again seized by a vision of the planet exploding. He notes how Unicron's strength grows ever greater and continues on. Arcee and Optimus Prime both voice their mistrust of the Decepticon leader, though they have no choice but to follow him. Unbeknownst to them, several strange, mechanical creatures observe the intruders into their dark domain.
Back at base, Ratchet and the humans watch a report that outlines how the planet's chaotic weather continues to spiral out of control. Despite June's efforts to lighten the mood, Fowler insists that something must be done—even if it means contacting his associates at the Pentagon. Fowler makes known his uneasiness about teaming up with Megatron, but Ratchet surprises the humans by explaining how such a situation has happened before. Ratchet relates how Optimus Prime and Megatron were once close friends, in the twilight hours of Cybertron's Golden Age.
The great Autobot leader was once named Orion Pax, a simple clerk in the Iacon Hall of Records. Learning of Cybertron's past, Orion grew concerned about the corruption affecting high places and the state of inequity in society. He became inspired by the revolutionary words of Megatronus, a gladiator who took his name from one of the thirteen original Primes. Megatronus gained a loyal following through his radical and innovative actions, Soundwave chief among their number. Over time, Megatronus became a mentor figure to Orion Pax and chose to shorten his name as he left the gladiatorial arena for the political one. Megatron appeared before the High Council, voicing his ideas for shaping a new Cybertron by violent means, and demanded to be named the next Prime. Orion protested against Megatron's suggestions before the Council, moving their sparks and minds as he unknowingly revealed himself to be the one worthy of the title. Megatron severed his ties to Orion and the Council, taking his "Decepticon" followers to begin the war that consumed Cybertron and vowing to claim the legendary Matrix of Leadership for himself. Hoping to reverse the damage that had poisoned the planet, Orion journeyed to Cybertron's Core, where he found himself before the spark of Primus, the creator of all Cybertronians. Primus sensed the purity of Orion's own spark and bestowed upon him the legendary Matrix, transforming him into Optimus Prime.
In the present, Miko and Jack question Optimus' plan to give the Matrix to the Earth's core, asking what could possibly stop Megatron from attempting to claim it for himself now. Ratchet darkly replies that Megatron only intends to save the Earth so that he may conquer it at a later date.
As they near Unicron's spark, Bulkhead begins to feel the draining effects of the Dark Energon. Bumblebee and Arcee help him a short way across the catwalks, but Megatron soon comes to a halt ahead with the realization that Unicron is preparing to expel them. A huge number of Unicron's drones suddenly swarm into view, surrounding Megatron and the Autobots. They engage the drones in fierce battle, blasting and slashing through their attackers. Arcee is knocked to a lower level, not long before the Dark Energon clouds Bulkhead's vision. He stumbles from the catwalk but manages to grab hold of the edge, and is seized by Bumblebee before he can tumble to his death. Optimus and Megatron fight back-to-back, managing to hold their own against the drones in a spectacular display of effective—if uneasy—teamwork. Bumblebee struggles to hold onto Bulkhead, who insists that the scout lets him go. Optimus seizes Bulkhead just as Bumblebee loses his grip, and hauls him up to safety. As the group quickly becomes overwhelmed, Arcee hitches a ride on one of the drones to catch up with the others and beat a swift retreat with them.
Aboard the Nemesis, Airachnid outlines the questionable nature of their leader's recent behaviour. Knock Out asks whether she is suggesting that they abandon Lord Megatron. Airachnid explains how Megatron's undetectable signal implies that he is either offline or at the mercy of Unicron—neither scenario being in the best interests of the Decepticons. She suggests an exodus from Earth, and receives no protests from the surrounding Vehicons. However, her order to retreat to Regulon Four is denied by Soundwave, who silently challenges her authority. When he refuses her demand to step aside, she leaps to attack him. Soundwave easily blocks every one of her blows, before lifting her clean into the air. He hurls her back, deploying Laserbeak to stun Airachnid in a sudden sneak attack. Pinned under Soundwave's foot, much to Knock Out's amusement, Airachnid relinquishes command to the intelligence officer.
Back in the Autobot base, Ratchet notes he has lost the others' communication links and life signals, most likely caused by interference from the electromagnetic anomalies. Miko asks how they are supposed to know when the others are ready for pickup if contact is impossible, but Ratchet is prevented from responding by the sound of Jack tapping the Ground Bridge key against a railing. Ratchet reveals that the object is actually the Key to Vector Sigma—one of Cybertron's most precious relics. Ratchet then realizes that Optimus entrusted the key to Jack because he did not plan on returning from the planet's core.
Megatron is gripped by yet another painful vision of Unicron whilst he and the Autobots are backed into an enclosed chamber by the attacking drones. Unicron orders him to destroy Optimus. Instead, Megatron saves the Autobot leader by blasting an oncoming drone. He then indicates a closed doorway nearby, stating that Unicron's spark lies just beyond. He explains that, to pass through, they must fool Unicron into believing that they pose no danger, and moves his Dark Energon-infused chest up to the door. It opens in response, and Optimus orders the others to remain outside and provide cover fire while he and Megatron advance.
The passageway beyond leads directly into Unicron's spark chamber, where Optimus prepares to expose the Matrix within his chest. Unicron's spark reacts, striking both invaders with its energy. Unicron again orders Megatron to kill Optimus, forcing him to unsheathe his blade and approach the weakened Prime. Megatron struggles against him, declaring himself to be under the command of no-one. His resistance provokes only an onslaught of pain and a furious reaction from the Chaos Bringer.
The volcano outside erupts violently, and the ground enclosing the Autobot base begins to quake. Ratchet tells the humans to take cover, and he moves to shield them from falling debris.
Unicron's spark adopts the appearance of a face as Megatron is seemingly freed from his control. Optimus calls upon the power of the Matrix of Leadership, but hesitates as Unicron possesses Megatron's body in a veil of purple flame and declares his own invincibility. Optimus cuts short Unicron's desire to pull the Earth into chaos, and he rises to his feet as he becomes surrounded by a brilliant blue light. Optimus fires the power of the Matrix from his chest directly into Unicron's spark, the resulting wave of energy knocking Megatron back off his feet. His energy drained, Optimus falls to his knees, and Unicron's spark emits a final wail of pain before vanishing into oblivion.
The drones outside suddenly fall from the air, lifeless. The volcano, along with all of the Earth's other natural phenomena, subside back to normality. Ratchet and the humans watch as the monitors flicker online, rejoicing as their team's life signals are all safely re-established. Aboard the Nemesis, however, Soundwave also detects the signature of the Decepticon leader.
Megatron rights himself in Unicron's now-empty spark chamber, inspecting Optimus' steaming body for a moment before unsheathing his blade. Optimus gazes blearily up at the approaching Decepticon, then addresses him as "Megatronus" and asks where they are. Surprised, Megatron retracts his weapon and helps the Autobot to his feet. Bumblebee, Bulkhead and Arcee soon burst through the wall to assist, but Optimus does not recognise them. A Ground Bridge suddenly opens nearby; Megatron claims that the Autobots are their sworn enemies and provides cover fire as Optimus heads for the vortex. Optimus blankly meets Bumblebee's devastated gaze for a split second before disappearing through the Bridge. Megatron follows, leaving the shocked Autobots alone in the empty chamber.
Ratchet Ground Bridges the team back to base, but is anxious to see that Optimus is not with them. They explain that Optimus is still alive, but did not even know his own name. Ratchet realizes that surrendering the Matrix of Leadership caused their leader to lose not only the wisdom of the Primes, but his own memories as well.
Knock Out and the other Decepticons, minus Airachnid, welcome Megatron back aboard the Nemesis. Megatron steps aside to allow Optimus through, and Breakdown automatically moves to attack. Megatron halts him, insisting that this is no way to treat a "long-lost comrade", and declares that Orion Pax is one of them.
To be continued…
- Art Shift: During Ratchet's Flash Back of how the war began. It looks quite nice.
- Back-to-Back Badasses: Pulled off awesomely by Optimus and Megatron against Unicron's antibodies.
- Beware the Quiet Ones: And how. Lampshaded by Knock Out.
- Bittersweet Ending: Unicron is defeated and the Earth is safe, but Optimus loses his memories of being a Prime and leaves with his old friend Megatron(us).
- Laser-Guided Amnesia: When Optimus gives up the Matrix of Leadership to defeat Unicron, he loses all his memories and reverts mentally back to the time when he was Orion Pax and was friends with Megatron(us).
- No Ontological Inertia: When Unicron was defeated, all the natural disasters he was causing on Earth simply disappeared.
- Oh Crap: Both Autobots and Decepticons get this reaction when they realize that Optimus has lost his memories and "switched" sides.
- Ship Tease: Between June and Agent Fower, where the latter gave her giant hug after Unicron was defeated, only to let her go in embarassment.
- The Starscream: With Megatron gone, Airachnid does her best to fill the Trope Namer's shoes. Soundwave disagrees.
- Wham! Line:
Optimus Prime: " Where are we, Megatronus?"