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Hedron tries to build a tower on the one planet he's not allowed: Earth. The Fates are furious and use the Infinity Stones to shatter him to pieces. They then task Ozpin with hiding the Reality Shards across the world to make sure that no one can ever revive Hedron.
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Trebla sealed Albert away for 10,000 years.
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Trazio joins the Red Umbra and tries to become the leader so that he can do a successful evil plan.
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Dimentio steals The Great Funny's Hat and plants a Floro Sprout in his head to control him.
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Sherlock finds Daffy in the Land of X-Box and has him arrested for running a fake Pokémon lab and attempted murder.
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Sherlock and the player find Moriarty in the Baker City Gym; Moriarty explains some of his plan.
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Discord battles the player as the eighth and final Gym Leader, but after he loses, he throws the player into another dimension.
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Using the time when the Player isn't there to interfere, The Great Funny sends his commanders to every town in Alternia and takes over the whole region.
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Moriarty takes a helicopter to Finale City in the Perio region and talks to Roman Torchwick and Grant Ward about the GRIMM Rift. Radcliffe calls him and tells him that he can make LMDs. "SAY THAT AGAIN!"
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Bugs finds the Player somewhere in the Furthest Ring and brings them to his house in Castle Town. In the week that they were gone, however, The Great Funny took over the entire Alternia region.
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...That.
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The Player climbs the Tower of Harmony to find Tai Lung, and battles him to prove that they are worthy. After they are victorious, Tai Lung offers them one of two legendary Pokémon: Reshiram and Zekrom.
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and uses it to try to make the Portal of Power.
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The Player finally arrives in Ponyville and challenges Discord with their new legendary dragon. After Discord loses, he realizes how much he misses his friends and goes back to Equestria.
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At the top of The Great Funny's Castle, Moriarty shoots Sherlock; but Sherlock rigged the gun to explode when it was shot, so Moriarty exploded. Unknown to the Player and Sherlock however, that was actually a robot version of Moriarty created by Meka Man.
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Kaos exploits the Portal of Power to create Organization XIV.
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During the Jade Tournament, the Jade Tower explodes and Daffy steals the Soul Stone. Shifu tells the Player to find Oogway so that they can combat Daffy's newfound chi power.
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A bunch of Meka Man's robots blow up.
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The Player uses the three MacGuffins Oogway hid on Isle Delfino to go to the Spirit World. Oogway then gives the Player a part of the other legendary dragon to make theirs more powerful.
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The player encounters Daffy on Mt. Animus, where he is training to do battle with the Fates. Bugs shows up to stop him, but Chara tries to use the Soul Stone to separate from the player. Then Gaster returns but is immediately defeated.
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The player gets a Pokémon from Flynn and is sent on a long training journey to defeat Organization XIV.
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Using :chocmilk: from Aperture Science, Organization XIV weaponizes dark matter.
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...That.
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After Herbert was sent flying into the Furthest Ring because his universe exploded, Bugs showed up to save the day.
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Bugs learns of the Dark Nebula's plan, but before he can tell anyone, he gets venomed by Cipher... But then he takes over Cipher and cuts their connection to the Dark Nebula.
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...That.
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Bugs takes over Cipher so they don't give the Dark Nebula any more venom.
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Dark Fawful screws up the entire plan by using his Vacuum Helmet to suck up all the Dark Matter in the region, and then explodes.
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You stop John from randomly blowing up the region... Yay?
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...oh, for f-
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After finding out that Bugs is in the Dark Dimension, you travel back to Caelum Town. Flynn comes to your house and reveals that he has the Space Stone to Daffy. Then you go to Lab XIV and use the Portal of Power to travel to the Dark Dimension.
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After a lot of battles, Cipher is defeated. Bugs doesn't remember anything that happened before he turned evil, including the knowledge about the Dark Nebula's plans. Daffy uses the Space Stone to return you to the Pokémon universe.
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Dimentio and the Dark Nebula go to Oraculum City's Ancient Library (not Refurbished) and steal the Dark Prognosticus.
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The Dark Nebula go to the Temple of the Heartless to find the Chaos Heart.
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The Dark Nebula tries to unleash Telozois using the Space Stone and the Chaos Heart, but the player is able to stop it. Dimentio then uses the Chaos Heart and Mr. L to turn into Super Dimentio and fights the player. Edward uses Human Transmutation to banish Dimentio to the Gate. The Phoenix Foundation Headquarters is consumed by Truth.
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Cyrus, Bugs, and Daffy visit Caelum Town to recruit Flynn to become an Infinity Guardian. They also explain a bunch of cosmicyness to Zeng.
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D-DUUUUUUDE! Dude...
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Team GRIMM use up all of the power in Finale Coliseum to power the GRIMM Rift and go to the Furthest Ring.