All but Thor board a helicopter and take off in search of Doom's flying fortress. When they find it, it latches onto them with a grappling beam. Everyone is frightened by this sign of power, except for the Hulk who leaps out of the helicopter and smashes his way into the aircraft.
Hulk takes off and starts to hunt through the ship by himself. Thor is upset, as he doesn't think that this is how a team should act but Iron Man thinks that splitting up is a good idea. So, each member of the team heads off in their own direction, except for The Wasp who is instructed to stay with the helicopter and protect the major. She reluctantly agrees, but as soon as the rest of the team is gone, Major Bowman sprays her with a gas that knocks her out. In doing so, he reveals that he's working for Dr. Doom!
While this is going on, the Hulk has discovered a bright and shiny room. When he enters it, he slips on the teflon floor and his kept in the air due to high pressure jets that were hidden in the walls. This effectively incapacitates him. Thor walks into another room wherein power spheres swarm around him and stop him from progressing forward. Dr. Doom is monitoring all of this, and notes that those power spheres were created to destroy the entire Fantastic Four. As he says this, Iron Man stumbles upon a room that seems to hold Doom. He stealthily approaches Doom's motionless figure, only to have it whip around and reveal itself to be a power draining robot. Without power, the suit won't be able to keep Iron Man's heart beating!
Ant-Man fares better. He stumbles across the real Major Bowman, and frees him from the ropes that bind him. Doom then reveals himself to Ant-Man via a television monitor in the room. He explains that he has split the team up in order to defeat them, and that he has The Wasp by his side in a small glass container. Gas begins to enter the room, and Bowman begins to despair. But, Ant-Man has a plan. He takes a pill and removes his helmet. Then, instead of shrinking, he grows to a much larger size and breaks through the ceiling creating an escape route for Bowman and himself.
Once free, they set about rescuing the rest of the team. First, the newly christened Giant Man pulls the Hulk out of the trap that he was stuck in. The Hulk is dizzy, and is sick all over the floor, but is ready for action. They next come across Thor who manages to use his hammer to free himself from the power spheres just as they are about to destroy him. Then, they find the room in which the robot is draining the power out of Iron Man. Hulk smashes through the mechanical fiend, and Thor creates a lightning bolt that restores all of Iron Man's power. Now, the team mostly reassembled, they make their way to Doom's chambers to rescue the Wasp.
They arrive just as Doom is about to broadcast a message to the world about his triumph over the Avengers. Thor lets his hammer fly and it smashes through the camera and the glass prison of the Wasp. Thor then launches his hammer at Doom himself, but it is deflected by a force field! As Iron Man disables that, Doom flees through a hidden tube in the floor. The Hulk smashes through the floor to chase after him, and receives an energy blast to the face from Doom's hand. This only makes the green goliath angry, and he charges forward. Iron Man tries to stop him, but is too late. The Hulk rips Doom's head from his shoulders! Iron Man is relieved to discover that this was just a robot, while the Hulk is vaguely disappointed. Suddenly, Giant Man and the Wasp come running down the corridor. Doom is destroying the ship with them all aboard.
The team finds one escape pod, and after some debate about who should use it the Hulk shoves Major Bowman into it and launches it. The rest of the team leap out the side, with the flyers carrying the non-flyers. When they land, they watch Doom's flying fortress crash into the ocean. Giant Man reveals that the Wasp informed him through their insectoid connection where the rest of the team was being kept. She knew this because she had an up close look at all of Doom's monitors. They are happy their second mission was successful but are left to wonder whether they ever really faced Doom at all.
Meanwhile, Dr. Doom watches all this from a safe distance with a new respect for these foes.