The cutscene starts out with Nick Fury establishing his fears about Dr. Doom's means to take over the world, and also introduces you to Iron Man's department, called the Stark Tower. It's a good spot where you can save your progress and do some activities before you go on to your next mission. You can do trivia, simulation, or look at pictures and videos.
The only side-missions are getting the decryption module from Black Widow to The Vision and finding Dr. Pym's helmet on the Omega Base. Unfortunately you can't go into Iron Man's lab until you complete the Omega Base mission.
Lastly, when you talk to Wingfoot, you'll ask him to find someone to examine Black Widow's laptop. When you are finished exploring this area, you should be ready to start on the next mission. On a side note, the Torch has a unique dialogue with him.
Also if you choose Elektra, you have different dialogue with Black Widow. So does Deadpool as well.