The cutscene shows Dr Doom using his powers to turn everything into Dr Dooms villanous views, turning every superhero into his supervillains.
You're going to revisit Stark Tower once more but with an empty room and the colour's has changed. Firstly marked with an "X" on all three consoles, you are to activate them to restore power. Then Nick Fury get's captured. So you go into Iron Man's Lab to save Nick Fury. But Nick is able to show that he has the energy inside to take care of Doom's minions. Dr Pym locks down the lab and your team has three minutes to hold off until he uses the EMP blast. Once its finished, take care of the remaining robots before you leave for the final briefing.
Before you leave, talk to Dr Pym for a final item quest. The dampener is near the Trivial console which is where Vision used to be when you first see this place and the manual near Black Widow on the table. Bring those two items to Dr Pym for the item which would work against Dr Doom.
Once you're done looking around Dr Doom's vision of Stark Tower, Fury will transport your team for a final confrontation.