The game picks up directly where the movie ended, as The Underminer drills out of the ground and declares his intention to rule the world. The Incredibles prepare to battle him when Frozone arrives. Mr. Incredible orders the rest of the Incredibles to take care of the Underminer's minions while he and Frozone defeat him. The two reach the Underminer's machine, but he quickly escapes underground. Mr. Incredible and Frozone pursue him. The two discover a computer containing the Underminer's plans and learn that he has created the Magnomizer, intending to reverse the position of the earth's crust and fill the sky with extreme pollution to create an artificial underground.
Mr. Incredible and Frozone make their way to the Sludge Station, where the Magnomizer is located. After defeating the Magnomizer Guardian, they reach the roof of the Magnomizer and destroy it. As the entire Magnomizer building begins to collapse, Mr. Incredible and Frozone quickly escape through a giant drill, and it falls down a deep pit the machine makes when it falls through the ground. The Underminer, aware that Mr. Incredible and Frozone have destroyed the Magnomizer, activates the Crustodian, his most powerful robot. The Underminer begins his backup plan to create 100 giant Gilgenbots to conquer the world with. Mr. Incredible and Frozone fight their way to the Crustodian, destroying three Gilgenbots in the process. The Crustodian decides to cover up its failure by destroying the other 96 Gilgenbots. After defeating the Crustodian, who escapes, Mr. Incredible and Frozone take an elevator down to an underwater plant that originally supplied power to the Magnomizer, and now powers the Corrupterator, a giant machine meant to help the Underminer further his world-dominating goals.