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Season 1

  1. A Better Day: The first appearance of all the characters. Master Xandred tries to interfere with peace, so he teams up with Grimlord and KOMPLEX in order to take over Toontown. So Optimus Prime formed his own terrific three out of himself, He-Man, and the Brave Little Toaster in order to save Toontown.
  2. A Darker Night: Nightmare Moon appears, and kills the president of Toontown. Toontown will soon elect someone as president.
  3. Vampires in Love: Dracula and Lilith are in love.
  4. Mater Sees All: Mater joins the team.
  5. Sakharine: The evil Ivanovich Sakharine tries to trap Mrs. Brisby and brainwash her son, Martin, into evil.
  6. Martin Brisby: Now evil, Martin Brisby is commanded by Sakharine to cause trouble in Nimh.
  7. Fox Box: Wayne Cramp, a new threat, tries to destroy the Fox Box, the main channel the heroes watch.
  8. Rocked and Bullied: Rocky and Bullwinkle try to save their friends from Xandred.
  9. Bucky joins the Team: Bucky O'Hare joins the group of heroes.
  10. All Are Apes: Captain Simian joins Optimus in his quest to destroy Lord Nebula.
  11. Surrender or Pay The Consequences: Overlord, ruler of the Spiral Zone, appears, and tries to team up with KOMPLEX in order to cause trouble for our heroes.
  12. Animeland: Sailor Moon joins the team.
  13. Red as a Rocket Raccoon: Rocket Raccoon defeats Overlord in a gladiatorial battle.
  14. Megatron: Megatron and Ultron, his brother, appear to haunt the memories of Optimus Prime.
  15. Gore, Blood, Violence, Strong Language, and Sex: Unusual things are going on at Toontown in the form of being mature with the South Park Kids in town.
  16. Phantom: The Phantom of the Opera haunts the Opera House once again.
  17. Townsville's Going Down: Dr. Blowhole brings down Townsville with the Legion of Doom, which consists of himself, Queen Beryl, Bane, Bizarro, Dr. Doom, and Marvin the Martian.
  18. Evil Returns: Evil the Cat has returned for revenge against Optimus Prime.
  19. All is Discord: Discord turns Toontown into a place of evil.
  20. House of Mouse: The House of Mouse first appears in this episode. Electra Woman and Dyna Girl kick Pete out of the clubhouse.
  21. Stadium Supreme: The heroes build a Stadium Supreme, a 6-stadium complex.
  22. Helping Hand: Krulos and his villain army lose to Super Soldier, the Amalgam superhero.
  23. Seperate!: Super Soldier splits into Superman and Captain America.
  24. The Evil Superboy: Superboy-Prime attacks the city, and only Optimus can stop him.
  25. Transforming Their Evil Fortress: When the villains leave the castle with the security cameras switched off unnoticed, the heroes transform the Fortress That Never Was into a Castle That Actually Always Forever Was.
  26. National Anthem: All the national anthems of the world are stolen by Mephiles, and only Optimus can save them.
  27. Pee Dog: When a male dog is frozen in time while lifting its leg on a hydrant, Optimus reveals that it was turned to bronze, and puts it in a Brussels street, calling it Zinneke Pis.
  28. Shark: Great White Shark appears, and tackles Optimus's last hopes, the Street Sharks.
  29. We are Mice: The evil Pinky and the Brain appear to haunt Optimus forever, and only the Biker Mice From Mars can stop them.
  30. Road Truckers: The Road Rovers and Silverhawks warn Optimus of Mumm-Ra, who is threatening the city.
  31. Il Muto: The fictious opera comes to be! While Optimus sees it, the Phantom of the Opera intervines. Did he not instruct that Box Five was to be kept empty?
  32. Dynamite: Baron Silas Greenback came back to throw dynamite at our heroes, and only Optimus can stop him.
  33. Sit on Chairface: Chairface Chippendale tackles Danger Mouse and Captain Scarlet.
  34. Heavy Duty: The G.I. Joes join Optimus.
  35. Dirty Earthworm: Earthworm Jim joins Optimus for the war against Psy-Crow.
  36. Polluted: Megatron and Queen Beryl have Sinestro's Power Rings and summon Captain Pollution.
  37. Darkstorm VS Firestorm: Firestorm is up against Darkstorm the Tyrant.
  38. What If?: Superted is bought back to life by the Pagemaster.
  39. Bananas: Bananaman first appears.
  40. Continue?: Optimus is trapped within the world of Weyard.
  41. RPG: Isaac and his son Matthew join Optimus and his friends on his travels around Weyard.
  42. Hannibal: Hannibal Lector is released from prison.
  43. House of Villains: The House of Mouse is taken over by the 666 Villains! What shall Optimus do?
  44. Solus: Solus, an evil alien, tries to kill Optimus.
  45. Farewell, Whitney Houston: This episode is dedicated to the memories of every single person that has died in 2012.
  46. Deadworld: Optimus travels to the Deadworld in order to save Whitney Houston. However, it is run by ghosts and zombies of the billions of people and animals who have died so far, including the Deadworld's king, Abel, who was the first to be murdered by Cain, who became Master Xandred.
  47. He's Dead, Jim: The Star Trek Crew recover the real-life dead bodies of Whitney Houston, Michael Jackson, Heath Ledger, and Lonesome George. All four of these famous figures died.
  48. Never Alone: Captain Hook kidnapps Optimus's children.
  49. Master Xandred Walks Alone: Master Xandred runs Toontownians away from their homes with his ten plagues.
  50. One Day More: The heroes and villains sing One Day More from Les Miserables.
  51. The Final Battle: The epic struggle between Optimus and Xandred begins.
  52. The End?: Master Xandred has been defeated at last. Toontown is safe. Optimus begins a new life as a tow truck he now scanned and transformed into. He-Man begins life as Adam. Toaster begins life as a real-life toaster. This is the end... for now...

Season 2

  1. Madness from the Skull: King Kong and the creatures of Skull Island invade Toontown
  2. His Resurrection: Master Xandred is resurrected by Gargamel, an evil sorcerer that found him.
  3. Gargamel: Gargamel is one of the most dangerous foes that optimis ever has seen.
  4. The Days of My Youth: Javert imprisons Princess What's-Her-Name. He turns her into a child.
  5. Time Runs Shorts: Optimus loses his shorts to Gargamel.
  6. He Gave Me Strength to Carry On: Jean Valjean is now fond of the Carry On series.
  7. Wounded and Wart-Filled: General Woundwort and his love the Snow Queen invade Narnia, so Optimus Prime needs to stop them with the help of Harry Potter!
  8. Claws: Claudandus, an evil cat, decides to kill without doubt. So, he kidnaps people, and Optimus can stop him.
  9. Revenge of Zygon: Zygon, an evil cyborg, has conquered Cybertron at last with the help of Megatron!
  10. Ice and Fire: Nekron appears to take down our heroes.
  11. Javertron: Megatron and Javert join forces.
  12. Heroes Alliance: Heroes Alliance members appear.
  13. Dark Force: The Dark Force first appears in this episode.
  14. Xena: Xena, the Warrior Princess, became an ally to Optimus.
  15. Mocked: Mok Swagger attacks Optimus.
  16. Nebula: Lord Nebula attacks the planet Cybertron! Only Captain Simian and the Autobots must stop him!
  17. Elseworlds?: What if the multiverse were eternal? What if Spider-Man had joined the Autobots?
  18. Mega Force: The Power Rangers Megaforce appear in this episode.

Season 3

  1. Crisis Part 1 : The Multiverses Live Perfectly And Created By God It Self Until... Anti-Monitor A Supremely Powerful Being Who controls the Antimatter Universe And. Destroying The Positive Matter Multiverse, Killing Untold Billions In The Process. Now All heroes and villains And The Forces of Evil Have To Stop The Anti-Monitor Before He destroying The Multiverse And Nothing will ever be the same. (Based On Crisis on Infinite Earths)
  2. . Crisis Part 2: Battle at the Dawn of Time! is here! God Has Been Defeat and Heroes' Loved Ones has died The Multiverses is now Two Some Heroes And Villains died And The final battle is near... (first appearance of a boy from Shocky Enthusia And Graham's number of MUGEN characters).
  3. Crisis Part 3: This is it the final battle Toontown vs Anti-Monitor who will win? who will die? (series finale) (Toontown wins)

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