Public opinion turns against Superheroes due to the collateral damage caused by their crime-fighting. After several lawsuits, the government initiates the Superhero Relocation Program, which forces Supers to permanently adhere to their secret identities and abandon their exploits. Fifteen years later, Bob and Helen Parr—formerly known as Mr. Incredible and Elastigirl—and their children Violet, Dash, and baby Jack-Jack are a suburban family living in Metroville. Although he loves his family, Bob resents the mundanity of his suburban lifestyle and white-collar job. Together with his best friend Lucius Best, formerly known as Frozone, Bob occasionally relives “the glory days” by moonlighting as a vigilante.
After his supervisor prevents him from stopping a mugging, Bob loses his temper and injures him, resulting in his dismissal. Returning home, Bob receives a message from a woman called Mirage, who gives him a mission to destroy a savage tripod-like robot, the Omnidroid, on the remote island of Nomanisan. Mr. Incredible battles and disables it by tricking it into ripping out its own power source.
Mr. Incredible finds the action and higher pay rejuvenating. He improves his relationship with his family and begins rigorous physical training while awaiting another assignment from Mirage over the next two months. Finding a tear in his super suit, he visits superhero costume designer Edna Mode to have it mended. Assuming that Helen knows what Bob is doing, Edna also makes suits for the rest of the family. Setting out for Nomanisan once again, Mr. Incredible discovers Mirage is working for Buddy Pine, a disaffected former fan whom he had rejected as his sidekick. Having adopted the alias of Syndrome, he has been perfecting the Omnidroid by hiring different superheroes to fight it, killing them in the process. Syndrome intends to send the perfected Omnidroid to Metroville, where he will secretly manipulate its controls to defeat it in public, becoming a “hero” himself. He will later sell his inventions so that everyone can become “super”, rendering the difference meaningless.
Helen visits Edna and learns what Bob has been up to. She activates a beacon Edna built into the suits to find Mr. Incredible, inadvertently causing him to be captured while infiltrating Syndrome’s base. Elastigirl borrows a private plane to travel to Nomanisan. She finds out that Violet and Dash have stowed away, leaving Jack-Jack with a babysitter. Elastigirl’s radio transmissions are picked up by Syndrome, who sends missiles to shoot her down. The plane is destroyed, but Elastigirl and the kids survive and use their powers to reach the island. Helen infiltrates the base and discovers Syndrome’s plan. Discontented with Syndrome’s indifference when her life was threatened, Mirage releases Mr. Incredible and informs him of his family’s survival. Helen arrives and races off with Mr. Incredible to find their children. Dash and Violet are chased by Syndrome’s guards, but fend them off with their powers before reuniting with their parents. Syndrome captures them all, leaving them imprisoned while he follows the rocket transporting the Omnidroid to Metroville.
The Incredibles escape to Metroville in another rocket with Mirage’s help. As per its programming, the Omnidroid recognizes Syndrome as a threat and shoots off the remote control on his wrist, making him incapable of controlling it and knocking him unconscious. The Incredibles and Frozone fight the Omnidroid together. Elastigirl acquires the remote control, allowing Mr. Incredible to use one of the robot’s claws to destroy its power source. Returning home, the Incredibles find Syndrome, who plans to kidnap Jack-Jack and raise him as his own sidekick out of revenge. As Syndrome flies up toward his jet, Jack-Jack’s own superpowers start to manifest and he escapes Syndrome in midair. Elastigirl catches Jack-Jack, and Mr. Incredible throws his car at Syndrome’s plane as he boards it. Syndrome is sucked into the jet’s turbine by his own cape and the plane explodes.
Three months later, the Incredibles witness the arrival of a supervillain called the Underminer. They put on their superhero masks, ready to face the new threat together as a family.