The game closely follows the plot of both of the Incredibles movies, but with some modification in order to be more child-friendly and adapt to the two players gameplay. In the story campaign, the player first goes through the second film's plot entirely, before going back to the first film. Some of the modifications made are:
During the level featuring Mr. Incredible's past (back when supers were legal), he works alongside Elastigirl to chase one of Bomb Voyage's minions across some rooftops, until they reach the bank, which Mr. Incredible enters alone, while Elastigirl goes to prepare for their wedding.
Inside the bank (during the same level), Mr. Incredible reluctantly works alongside Buddy Pine (whom he meets the first time instead of earlier in the movie) to defeat Bomb Voyage and his minions, who are using the bank's security against them.
The scene of Mr. Incredible saving a man from suicide is completely cut from the game.
When Mr. Incredible arrives for the first time on Nomanisan Island to defeat the Omnidroid, he runs into Frozone who was also hired to stop it. They work together to find the Omnidroid, but they discover that there are two of the robots, so they split up, each destroying one Omnidroid.
During Mr. Incredible's second visit on the island and after encountering Syndrome, he runs into Gazerbeam, who, unlike the movie, is alive. They work together to infiltrate Syndrome's base and reach his computer, but they are both captured. Gazerbeam is never seen in the game afterwards.
At the end of the first movie, Syndrome is still attacked by Jack-Jack with his new powers. However, unlike the movie, he doesn't die at all and instead accepts his defeat and goes into hiding. He later leads his own Crime Wave back in the open world, where he steals technology for a new Omnidroid.
The first level of the sequel takes place aboard the Underminer's driller tank, and has the Incredibles trying to stop it from crashing into the city hall after the Underminer escapes it. The process is significantly prolonged by numerous events that did not occur in the film to make the level substantially long enough, such as fights against the Underminer's minions and a moment where the tank is temporarily stopped and the player is then prompted to rescue some nearby civilians.
During the events of the second movie, Elastigirl works alongside a superhero named He-Lectrix to stop the high speed train, and later to save the Ambassador after Screenslaver took control of the planes.
Elastigirl does also work alongside another super, Reflux, to infiltrate Screenslaver's hideout and capture him.
The final battle on board the Everjust is shorter. It begins when Jack-Jack frees Elastigirl from Evelyn's hypno-goggles, before she and her children face off against a hypnotized Mr. Incredible and Frozone at the bridge. Frozone is then freed from the mind control next, but then a controlled Voyd steps in to fight the freed supers, using her teleportation powers to allow Mr. Incredible to ram the player characters in different directions. Once Frozone creates an ice ramp to lead Mr. Incredible into hitting Voyd, the two are freed from mind control. At this point, the player has beaten the Incredibles 2 portion of the story and watches the remaining part of the battle play out as one long cutscene: Evelyn then orders all remaining mind-controlled supers to attack, but they too are freed from mind control. Elastigirl then puts on her original red suit from the first film, and the supers all regroup and advance on Evelyn, apprehending her immediately before she could even get to the escape aircraft that was used in the film. With Evelyn captured, the supers then work together to steer the Everjust away from disaster and grind it to a halt.
The second movie has a slightly different ending, with the Parrs going to the cinema with Tony Rydinger where they all get mesmerized by the screen (probably indicating Screenslaver's return).

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