Dr Doom congratulates your team for Uatu's intervention in bringing your team back from the dead since the final confrontation of Loki and the invincible armour.
The first part leads to a simple puzzle of choosing a door. Obviously its the door which you can open to get to the next area which is the way you enter. Afterwards, the next area requires you to jump in to Doom's lair. It's not hard but if you're done on the first part, that's when you jump down.
Finding Dr Doom' Items
You're now on the stairs and you need to go up fighting more Dr Dooms toughest minions. The next area shows Dr Doom's statue. The upgrades are locked and the save point not accessible. Go to the top door on the right to acquire the items to unlock where Dr Doom is.
Go through what looks like Professor X's top floor mansion full of books. Find the bookcase which unlocks another section. You're going to deal with the dark version of the lighthearted superheroes.
First is Dark Captain America and Dark Colossus. They shouldn't be too difficult as long as your team is able to take them down. Once you defeat them, go to where the gauntlet is to go through another set of villains. And if you are Captain America, you get a different dialogue with the dark side.
Secondly is Dark Psylocke and Dark Cyclops. The good news is they fight separately, the bad news is to avoid falling to an upside dimension of the same spot fighting Dark Psylocke. Enter the Hall of Arms, take care of many more enemies before taking the armour that belongs to Dr Doom.
Continue into Dr Doom's Lab. Also as an option, look out for the Ultimate Nullifier. It's marked in an "X" and it's broken. After going through the platform, the last encounter is Dark Thor and Dark Spider-Man. A final sidequest is to use Dark Thor's weapon to free Odin. Also to get the Doom's mask and exit back to Castle Doom. Lastly, if you're Spider-Man, he'll have a different dialogue with the dark side.
The Dark Fantastic Four
The Doom statue will now open with glass broken and your last chance to save your progress through SHIELD access. Before you deal with Dr Doom himself, once you reach his lair, you have to take down the Dark Fantastic Four. It's a pain if you don't upgrade your team's defence and offence. So do your best to minimize casualties as they're needed for the final fight on Dr Doom.
Last Stand Against Dr Doom
Unfortunately, Dr Doom is invincible at the moment. Five "X"s is where you need to attack it. Take one step at a time as one of the Dark Fantastic Four will attack you each time. Once the "X"s gone, attack Dr Doom and rapidly press the button or shake the to steal his powers.
Now with his powers taken, you can finally beat him with everything your team got. Also the Dark Fantastic Four is easy to beat but respawn endlessly so you can ratchet up your health while taking down Doom's health. Continue meleeing in close range, long range and extreme attack to defeat Dr Doom.
The cutscene will show the aftermath of Dr Doom's last moment. Following is Uatu's view of what you did until the end credits. After the credits, you'll be back where you were. You can save and do any of the levels again with the exception of the major bosses no longer there and redo sidequests that you previously have acted or enacted, items missed or a superhero that you've chosen before like Nightcrawler and Jean Grey. Lastly a great chance to upgrade and change teams as you please.
If you think it's truly over, play "Marvel Ultimate Alliance 2" to find out what happens to the heroes who saved this world from Dr Doom.