So, searching through mcbasilrocks's tumblr account, I found a very exciting piece of information. Here it is.
OH. MY. GOD. You know how there was that huge thing over EM2 being unfinished? Well guess what I found on Wikipedia today? I was searching through the archives of the EM2 page (y'know, like you do) and found a really old plot summary written about 2 months after EM2 was announced, but was actually pulled by Disney themselves due to, I quote: ‘unauthorised leak’. Here it is.
The game is set some time after the original Epic Mickey. The Mad Doctor, whom Mickey defeated in the first game, mysteriously returns to the Wasteland, despite having been supposedly blown up in the first game. He claims to have realized the error of his ways, and offers to work with Oswald The Lucky Rabbit and the other residents of Wasteland to repair the damage recently caused by earthquakes in order to make amends. Giving him the benefit of the doubt, Oswald agrees. However, not long after accepting the Mad Doctor’s help, Wasteland begins to suffer even more damage than before. Becoming suspicious that the Mad Doctor is not keeping his side of the bargain, Gus the Gremlin, Oswald’s friend and advisor, and Ortensia, Oswald’s girlfriend/wife, decide to contact Mickey Mouse, who saved the Wasteland in the first game, to ask for his help. They do so, and Mickey, climbing through the same mirror that he ventured through in the first game, retrieves his magical paint-and-thinner-spraying paintbrush from Yen Sid’s workshop, after having it confiscated at the end of Epic Mickey. With Gus’s help, Mickey returns to the Wasteland to assist in uncovering the truth behind the Mad Doctor’s supposed reformation, teaming up with Oswald along the way.'
Ok, so more or less the same as our current EM2 plot, with a few minor tweaks. - Mickey enters Yen Sid's Workshop through his TV this time, as Yen Sid reverted Mickey's mirror to normal at the end of the first game. - The brush is found in the Brush Realm, an area close to, but not in Yen Sid's Workshop. However, now it starts getting interesting.
'The two later discover that the Mad Doctor has been using his offer of help to lure Mickey back into the Wasteland. Using Big Bad Pete as an undercover spy, he manages to trick the allies into believing the damage had been done by Gremlin Prescott, the grumpy caretaker of Wasteland’s Gag Factory, taking advantage of Prescott’s feelings of rejection towards Gus. However, Big Bad Pete promptly betrays the Mad Doctor once the Blotworx (a collaborative project between the two; a mixture of Blotlings and Beetleworx concocted in an old laboratory in Tomorrow City, intended to act as an army to take revenge against Wasteland) inadvertently send Prescott falling to his doom; Pete reveals he had ties with Prescott’s agenda and therefore aids Mickey and Oswald, revealing the secret of the Doc’s plans to lie at the heart of Dark Beauty Castle.
As Mickey and Oswald confront the Mad Doctor in Dark Beauty Castle, the Mad Doctor reveals his plan - to extract the essence of the Phantom Blot that Mickey soaked up upon being transported to Wasteland in Epic Mickey to resurrect the Blot. The Mad Doctor does so, and also removes Mickey’s Heart and uses its cartoon energy to restore power to the Blot. The earthquakes under Mean Street were caused by the Mad Doctor’s machines at work underground. The Blot reawakens, and, bursting through Mean Street, begins laying waste to the land. Realizing their mistake, Oswald and Mickey decide to make the ultimate sacrifice - destroy Mickey’s Heart, and the Blot with it. The pair take the Moonliner Rocket from Tomorrow City, and, with Ortensia and Gus’s help (as well as Pete; he cages the Mad Doctor, who escapes and merges with the Blot shortly after) to allow Mickey and Oswald to fend off the remaining Blotworx that were reborn in the blast), neutralize Mickey’s heart by overloading it with Thinner, thus eradicating the Blot and the Mad Doctor (who had been controlling the reborn Blot from the inside) in the explosion.
Dejected, Mickey comes to terms with the fact that he is now trapped in Wasteland. He heads to the peak of Mickeyjunk Mountain, where Yen Sid, the wizard and creator of Wasteland, touched that he made such a valiant sacrifice to save his friends, grants both him and Oswald a Heart, thus making them true brothers. The game ends with Mickey returning to the cartoon world, knowing that he can return to Wasteland at any time, and that Oswald can now leave if he wishes to. Mickey asks Oswald if he would like to come with him, but Oswald decides to stay, stating that the Wasteland is his home, and that he doesn’t want to leave Ortensia behind again. Mickey returns home as all the Wasteland residents bid him farewell. After the credits, a clip plays detailing the Wasteland’s fate depending on how the player played through the game. The clip changes according to the choices that Mickey made throughout the adventure.'
Ok so just to back up this, I found some images that correspond to some unused cutscenes from this story.
They show a battle scene in Tomorrow City, and Mickey trapped on a table in Dark Beauty Castle. This corresponds to the scene where Mickey fights the Blotworx in Tomorrow City, and when the the Mad Doctor tries to extract the essence of the Blot from Mickey.
Also, some concept art.
This's one shows Mickey and Oswald fighting Blotlings in Tomorrow City, with the Mad Doc trapped in the electric cage, and Pete overlooking the battle.