The cutscene with Nick Fury explains what you can do on the next mission. After the cutscene, you start inside the Omega Base. Early on, you'll meet up with Dum Dum Dugan, Wolverine's old ally, whom you need to protect for the first section of this level.
During your progress, you will not encounter just the troopers but with Super Soldiers as well. When you reach the engine area, Dugan has an idea to slow the Omega down by destroying the main engines. You'll find four of them marked with an "X".
Before you reach the other two engines, Crimson Dynamo stops you and challenges you to a fight. His attacks are electric attacks and missile from his suit. He will be overcome because your team of four would be able to attack him in all directions. It's worth noting that he is Iron Man's rival. The dialogue would be different if you choose Iron Man than anyone else at this moment.
After you defeat him and take out the two remaining engines, then take out the remaining enemies until you reach the console which isn't broken and Dugan will remain at this place to monitor the situation. Continue to the elevator which will take you outside at the top of the base.
Outside Omega Base
The camera view will be panning at the top and you won't be able to control it at this section. You're going to encounter troops with shields and a helicopter shooting you down. If you see a red circle, move out of the way! Continue through that area until you reach Project Labs.
In the lab, you can save at that moment before you continue on your mission. Your next encounter is with four Super Soldiers waking up in the lab after Mysterio mess with the console then let it blow up. The four Super Soldiers are tough but is still easy enough to overcome.
After you take out the Super Soldiers, you go through the level to meet Bruce Banner who's locked in his lab. Dugan tells you there's a gamma bomb somewhere in this area. Before you leave the lab, pick up the helmet that Hank Pym wanted you to find. Go to the next area and take care of two more Super Soldiers so that Bruce can go in and disable the gamma bomb. But you need to go to another area to deactivate the barrier so that Bruce can disable it. Afterwards, you tell Bruce to get out of the Omega Base so you can continue on your mission.
By the way, if Mr Fantastic is in your team, you will get to hear their unique dialogue.
Go to the "X" to meet Mysterio. Mysterio is Spiderman's rival. After the funny conversation between the two rivals, Mysterio uses the Hologram item to make two more replicas of himself. He'll continue to replicate until Mysterio himself is the last person standing. Defeat him before you continue on your mission.
With Mysterio gone, your team take the elevator for a breather. But MODOK announced that your team is a threat. So you have to take down more troopers and also encounter some bombs which would damage you if it blows up. You can just stay away and let it explode but to disarm it, press the action button and follow the button sequence. The Wii version would want you to follow the motion sequence instead.
When the lift stop. You go across to another lift. Although optional, you can go to the door in the middle and stop the Super Soldiers destroying the computer. On another lift, it's the same thing but at the same time, you'll encounter bombs to disarm.
Reaching for the Anti-aircraft Guns
The SHIELD agent in the next area would ask you to take out the helicopter with the only anti-aircraft gun which is at the farside of the area. So you go through the area but the helicopter blocked it by taking the side of the place near the stairs. The enemies at the top platform needs to be taken down so you can move the metal object through the rail that is broken, breaking the glass at the bottom which takes you inside the base. Take out more enemies inside than go out to where the anti-aircraft gun is. The helicopter releases some more enemies than goes up in the air. Another SHIELD agent tries to open an another area but the helicopter is hovering over that area.
The anti-aircraft gun is at the bottom platform of this area. You have 45 seconds to get to the anti-aircraft gun before your team and your allies are overpowered. However once you reach the gun, the cutscene automatically cuts in for you. So you don't have to worry about shooting down the helicopter. Then take down the remaining troopers before you confront MODOK.
Trivial Pursuit MODOK Style
MODOK will freeze your team on its place and forces you into trivial pursuit. It's multiple question based and its quite easy to answer. If you get it right, you move forward a few steps near the boss. If you get it wrong, you'll get electrocuted. Once you get three answers right, you'll go into battle with MODOK. He's far harder than Super Soldiers and will be accompanied by the troopers. However, if you upgraded your favourite superheroes strength, XP and defence, your hero would last longer and if you're low on health, the troopers will randomly release health and power. Once you are finished, taking out the enemies and defeating MODOK, go on the console to stop Omega Base from crashing through the dam. Nick Fury will confirm that your mission has finished and asked you to return to Stark Tower again.