The Bad Guy Wins is usually a definitive ending to a story.
This story, however, is when an alternate future, alternate timeline or parallel universe exists where the villain won.
Thus, this trope differs from The Bad Guy Wins in that it's a scenario that could potentially happen, rather than a scenario that has happened. In the regular timeline/universe, the villain in question has been defeated (or at least has yet to succeed at Taking Over The World).
A staple of this trope is taking the meekest and/or most laid-back member of the main cast, and make him/her the battle-scarred soldier leading the resistance.
While this is often a Bad Future, as this can also involve parallel universes, this is just as often a Bad Present.
Anime and Manga
- Future Trunks comes from an alternate timeline where Androids #17 and #18 have killed most of the Z-Fighters and plunged the Earth into a state of total chaos.
- Age of Apocalypse is an alternate timeline where Apocalypse took over Earth because of Charles Xavier's death in this universe, so Magneto leads the X-Men in the fight against Apocalypse.
- Days of Future Past is an alternate timeline where Sentinels have taken over the Earth and exterminated most of the superpowered population.
- The New 52: Future's End is an alternate timeline where Brother Eye took over Earth and most of the population was promptly subjected to Unwilling Roboticisation.
- Kim Possible: A Sitch in Time shows an alternate future where Kim's arch-nemesis, Shego, has successfully taken over the Earth.
- After Shrek makes a Deal with Rumplestiltskin to eliminate one day of Shrek's life in exchange for giving Shrek some much-needed peace and quiet, it's revealed that the day Rumplestiltskin eliminated is the day Shrek was born, creating an alternate timeline where Rumplestiltskin took over Duloch, Far Far Away and Shrek's swamp.
- Phineas and Ferb: Across the Second Dimension shows the Second Dimension, an alternate dimension where Dr. Doofenshmirtz succeeded at taking over the Tri-State Area.
- In Cinderella III: A Twist in Time, after Lady Tremaine steals the Fairy Godmother's wand, she uses its magic to create an alternate timeline where Anastasia married Prince Charming (and thus is heir to the throne of the kingdom).
- It's revealed that X-Men, X2, X-Men: The Last Stand, X-Men Origins: Wolverine, X-Men: First Class, The Wolverine and the "bad present" scenes of X-Men: Days of Future Past are all part of an alternate timeline where the Sentinels have taken over Earth and are systematically exterminating mutants. The "regular" timeline is made of the 70s scenes of Days of Future Past, the "good present" scenes of Days of Future Past, Deadpool, X-Men Apocalypse, Deadpool 2, The New Mutants and Dark Phoenix.
- The Star Trek Kelvin Timeline consists of three movies (Star Trek, Star Trek: Into Darkness and Star Trek Beyond) where the evil Romulan Nero, despite being defeated and killed in said timeline, still manages to destroy Planet Vulcan and wipe out pretty much the entire Vulcan race (as well as killing George Kirk by destroying the USS Kelvin, hence the name for this alternate timeline).
- In Back to the Future: Part II, the future Biff Tannen uses the Delorean to go back in time to 1955 and give his younger self a sports almanac from the future. This creates an alternate timeline where Biff becomes so rich by betting on sports events depicted on the almanac that he takes over Hill Valley.
- One of the earliest examples of this trope is the movie It's a Wonderful Life, where the angel Clarence shows George Bailey an alternate timeline where Corrupt Corporate Executive Mr. Potter took over the entire town because George wasn't born in this timeline.
- In the Power Rangers Mystic Force two-parter "Dark Wish", Imperious get ahold of Jenji's lamp. Despite Jenji being a Benevolent Genie, he still has to grant Imperious' wish, creating an alternate timeline where Imperious took over Earth.
- Legends of Tomorrow: At the end of the Season 5, we see an alternate reality where the Fates took over Earth.
- The Trope Namer is the My Little Pony: Friendship Is Magic episode "The Cutie Remark". Due to Starlight Glimmer travelling back in time to prevent Rainbow Dash's first Sonic Rainboom, several alternate timelines are created: one where King Sombra won, another where Queen Chrysalis won, another where Nightmare Moon won, another where Discord won, and another where the Flim Flam Brothers won. The final timeline, a lifeless wasteland, is implied to be one where Princess Celestia's Super-Powered Evil Side "Daybreaker" emerged and burned all of Equestria to the ground.
- An episode of Gargoyles shows an alternate future where a cybernetic David Xanatos took over Earth.
- An episode of Xiaolin Showdown showed an alternate future where an older Jack Spicer took over Earth because Omi wasn't there to stop him.