Through all of this, there's also the question of if the Mad Doctor's evil plot should remain the same. Obviously there has to be some changes now that Prescott wasn't defeated on schedule, but should anything else have changed?
Let's start by examining the Mad Doctor's motivations in EM1 and EM2. His motivations are similar, but also pretty different between the two games when you think about it.
In EM1, his main motivation is wanting to rule Wasteland. If we look at all of his actions through this lens, it puts a lot of them in a more sinister light:
When the Mad Doctor first arrived in Wasteland, he wouldn't have had any resources whatsoever to try to conquer it with. And there's no way that Oswald would have sat idly by while the Mad Doctor tried to build up those resources. Unless Oswald didn't realize what they were for, that is. So the Mad Doctor bides his time. He befriends Oswald instead of making an enemy out of him straight away and slowly but surely gains his trust. He does nice things for Oswald like helping him build Animatronic Goofy, Donald, and Daisy for seemingly no other reason than to make Oswald happy, and he pitches the Beetleworx as cheerful little helpers that are meant to make life easier for everyone. With how much the Mad Doctor was able to take over after he switched sides, I imagine that Oswald trusted the Mad Doctor enough to let him do what he wanted with very little oversight. Had the Blot not happened, the Mad Doctor would have tried to take over on his own once he felt like he had everything he needed to overthrow Oswald.
But the Blot does happen, and suddenly, the Mad Doctor has another option. He doesn't have to play nice with Oswald anymore. So he switches sides. That doesn't mean he trusts the Blot to deliver on the power it promises him, though. He outright expects the Blot to betray him in the end when it sucks all the paint out of Wasteland, which is why he turns himself into an animatronic. He reasons that once the Blot wins, animatronics will be the only survivors, and he'll rule over Wasteland as its Mechanical King.
With that said, one has to wonder if this is really how he wanted to rule Wasteland. Who would he even be ruling over? The only animatronics we see are the Beetleworx, the Pirates, and Animatronic Goofy, Daisy, and Donald. But this might just be him making the best of a less than ideal situation. Being the mechanical genius that he is, he could always build animatronic versions of Oswald and the other toons if he wanted to.
The ironic thing about this is that if the Mad Doctor hadn't switched sides and had worked with Oswald instead, they likely could have defeated the Blot together. But the Mad Doctor is nothing if not a coward, and rather than risk himself, he wanted to be on what he saw as the winning side.
Except, after the Mad Doctor switches sides, Oswald still manages to bottle up the Blot. And fast-forwarding to years later when the events of EM1 start, Oswald and the other toons are still putting up enough of a fight that the Mad Doctor and the Blot haven't completely taken over.
So then we have the events of EM1. The Mad Doctor does try to steal Mickey's heart after he arrives in Wasteland, but I got the impression that the Mad Doctor did this for the Blot, not so that he could use it to escape Wasteland like he wants to in EM2. After Mickey escapes, we don't see the Mad Doctor again until his boss battle in the attic of the Lonesome Manor. Mickey and Gus send him flying, and unknown to us, he eventually crash lands in Autotopia where he immediately sets up shop.
This brings us to EM2, wherein the Mad Doctor's motivations have shifted from wanting to rule Wasteland, to wanting to leave Wasteland and become the greatest villain the Cartoon World has ever known. And right away, I have to ask why. Assuming that his motivation since arriving in Wasteland was to take it over, why give up on that now? Why does he suddenly want to be remembered? If being remembered is so important to him, then why didn't he try something like this earlier? If he can't even best Oswald and Mickey, then what makes him think he can make it as a villain in the Cartoon World? Wasteland is a much safer bet. Especially with the Blot gone. He does state that he plans on using the brush to make himself this great villain, but he seems to have forgotten that the brush actually belongs to Yin Sid, and Yin Sid certainly isn't going to let him keep it once he leaves Wasteland.
I'd also like to question if the Mad Doctor's plot to be remembered was really going to work or not. His final boss fight seems to imply that it did. He has his ride set to pull the Guardians out of Wasteland and he's ready to steal the brush from Mickey to become the greatest villain of all time when he enters the Cartoon World. But it's never explicitly confirmed that he successfully regained his heart. Could it be that he was bluffing? Can he even be properly remembered while he's still an animatronic and no longer a toon?
I can understand why the Mad Doctor doesn't want to be an animatronic anymore now that he's starting to break down and no longer needs to be one to protect himself from the Blot, but I can't help but wonder if wanting to leave Wasteland is really what his motivation should be right now.
Of course, just because his plan won't work out, that doesn't mean the Mad Doctor can't be confident that it will. Maybe he's tired of Wasteland. Maybe he wants to move on to bigger and better things.
But. Consider. Maybe instead of leaving, his real goal is more along the lines of getting rid of Oswald and Mickey. With his two biggest threats gone, then there will be no one that can stop him. And if anyone tries, the brush that he plans on stealing from Mickey will make him unstoppable. The only one that might be able to stop him is Yin Sid, but if the Blot and Mickey's Blot-induced rampage have proven anything, it's that Yin Sid isn't inclined to take action to help Wasteland no matter how badly it needs it.
With no one around to stop him, he has all the time he needs to bring any evil plan he can think of to fruition. He doesn't have to hide or scheme or do things in one fell swoop to avoid being stopped by the heroes. Instead of rushing off to the Cartoon World with the brush, he can find a way to replicate its powers and make it so Yen Sid can't take it from him if he ever gets bored ruling Wasteland and wants to move on.
That's where the whole "getting remembered" plot comes in. He may not plan on acting on it now, but it provides a distraction from his real goals and is an easy way to help sway Prescott to his side. Why Prescott? Because he's an easy target.
Prescott considers himself to be a misunderstood genius who isn't getting the attention he deserves and is having his talents wasted. So what would be easier for the Mad Doctor than promising Prescott that he has a way to get them both remembered? Even if that doesn't end up working, the Mad Doctor can also promise that Prescott's talents will never go to waste and he'll get the recognition he deserves if the Mad Doctor is made the ruler of Wasteland.
The Mad Doctor needs Prescott because he can't build the TV that broadcasts the show on his own. Or at least, I assume that's the case since he didn't build it himself. The same could possibly be said of inventing something that will force the Guardians to make the Mad Doctor a toon again. Prescott is also just a good pawn to have. It the Blotworx Dragon hadn't done Oswald in, then Prescott's boss fight likely would have.
And while Mickey and Oswald are busy, the Mad Doctor and Prescott prepare for one final, deadly confrontation.
Why would the Mad Doctor's plan have changed like this? He was inspired by watching Mickey's Blot-induced rampage. Mickey certainly took care of a lot of his problems by thinning them out. And while I'm not so sure Mickey actually permanently killed anyone since paint can restore a thinned out toon, it gave the Mad Doctor the idea of permanently taking care of his problems, namely Mickey and Oswald. This isn't to say he's never tried to kill them before, but it was always in a "because you're getting in my way and trying to stop me" kind of way, not the main goal. Once he takes care of them, he'll be free to do just about anything he wants at his leisure. Which I'm sure is a relief after having to play nice with Oswald for years and then having to worry about the Blot for years after that. He just needs that brush first.
But if the Mad Doctor's whole plan centers on getting rid of Oswald and Mickey, then why not kill Oswald after managing to take him down? That would have been the next step, but Mickey didn't show up with the brush when he was supposed to. If he's not going to show up just because Wasteland is in trouble, then maybe he'll show up because his brother is in trouble.
Or at least, that's what the Mad Doctor tells himself. He could have just went ahead and killed Oswald anyway and pretended to be holding him prisoner to the same effect. But if Mickey does show up and finds out that the Mad Doctor killed his brother, the Mad Doctor's going to have an angry mouse with the powers of creation/destruction coming after him. And more than that, it's personal with Oswald.
The Mad Doctor is someone who revels in his villainy and embraces the melodrama of it all. He's been trying to defeat Oswald for decades, and now that he finally has Oswald in his clutches, there's no way he can resist the opportunity to torment him. Why simply kill him when he can do something far, far worse? Because when you pretend to be somebody's friend for years and they grow to trust you, you learn all kinds of things about them. Like what they're afraid of.
What is Oswald afraid of? Being helpless is a given. Not being able to help the people he loves is another. But more than anything else, Oswald fears being left alone. Reduced to nothing more than a head, the rest of his body scattered across Wasteland, Oswald hasn't been this alone and helpless since he lost Ortensia.
Can we just stop for a moment to imagine the situation Oswald is in? He is completely alone and unable to move. He can't do anything, least of all help himself. Without his ears, the only thing he's capable of hearing is the sound of his own voice. He's back at the place he spent decades isolating himself at to make sure that the Blot didn't escape its bottle, but now Mickeyjunk Mountain has become his prison instead. The Mad Doctor hasn't left him unguarded, and until Mickey gets there, is there really any toon in Wasteland that is both capable of helping him and would care to do so? The Gremlins and Animatronic Goofy/Daisy/Donald would get themselves caught, the Petes and Lonesome Ghosts wouldn't care, and the Pirates are, well, pirates. There's Ortensia, but between EM1 and EM2 we never get to see her in action so we have no idea how well she could handle herself. And that's assuming they even know that his body has been scattered around Wasteland and his head is at Mickeyjunk Mountain. The Mad Doctor is only going to tell Mickey that because he's trying to lure Mickey into a trap.
The Mad Doctor might have let it slip that Oswald is being used as bait to lure Mickey here, but isn't that a laugh? Oswald is certain that Mickey doesn't care about him and would sooner use the opportunity to finish him off. As far as Oswald is aware, he's never getting out of here. And to top it all off, I imagine that Oswald would have been here for at least a day or two since it would take time for Gus to contact Mickey, Mickey to arrive and find out where Oswald is being held, and for Mickey to find him.
And that's not even getting into how the Mad Doctor left him there to begin with. Because you just know that the Mad Doctor waited for Oswald to regain consciousness after having been knocked out during his capture before taking him apart. Being the melodramatic guy that he is, I'm sure the Mad Doctor had an entire victory speech planned, and to finish it all off, he probably left Oswald's head on his throne at Mickeyjunk Mountain himself.
Speaking of Oswald and the Mad Doctor's relationship, can you just imagine how much the Mad Doctor's betrayal must have hurt? Oswald was only a year old when he was abandoned by both of his dads, and with the alternate history this game seems to be running on, Oswald was forgotten not long afterwards. Not only that, but some two seconds after abandoning him, they made Mickey to replace him with. Oswald starts to make a life for himself in Wasteland, only for the Blot to happen. And then the Mad Doctor, someone Oswald considered to be one of his closest friends and one of his most valuable assets in winning the war against the Blot, suddenly reveals that "Oh by the way I never cared about you, I was never really your friend, and I was just plotting to overthrow you this whole time. What an idiot you turned out to be, huh? Excuse me while I go ruin everything we worked so hard to achieve."
On top of being abandoned by his dads, I can't imagine how much that must have shaken Oswald's confidence in forming relationships. Not to mention his ability to not just trust others, but trust that they actually care about him. And while I'm sure that Oswald knows that Ortensia, Gus, Animatronic Goofy/Daisy/Donald, and his children can't reach him, I think it says something that the person who does end up coming for him is Mickey.