The film opens with a series of short interviews between three famous superheroes including Mr. Incredible (Craig T. Nelson
), who possesses super strength, Elastigirl (Holly Hunter
), able to stretch her body with amazing flexibility, and Frozone (Samuel L. Jackson
), gifted with the ability to create ice.
While en route to a special event, Mr. Incredible picks up a police report of a high speed pursuit and suits up before driving to intersect it, seeing as he 'has time'. On the way, he is forced to stop and assist an old woman get her cat out of a tree. Mr. Incredible picks up the tree and shakes the cat out and into its owner's arms just in time to swing the tree onto the road and bring an abrupt halt to the car of the fleeing thieves. As another report comes in, he returns to his car to find a boy dressed in a superhero outfit sitting in the passenger seat. Recognizing the boy as Buddy (Jason Lee
), an over-enthusiastic fan who declares to be Mr. Incredibles new ward, 'Incredi-boy', Mr. Incredible ejects him out of the car. On a nearby rooftop, he confronts a burglar sifting through stolen purses but the man is knocked out by the outstretched fist of Elastigirl. Mr. Incredible and Elastigirl engage in some playful banter before she runs off. As Mr. Incredible secures the burglar, Frozone glides by on a bridge of ice, shouting out a reminder that he needs to 'get ready'. However, Mr. Incredible's attention is suddenly drawn to an adjacent building where spotlights illuminate a man preparing to jump to his death. Mr. Incredible foils the suicide attempt by launching himself off the roof and knocking the falling man into an office of the building. He places the injured man aside when he senses something else amiss and walks to a nearby vault that is suddenly blasted open. The super villain, Bomb Voyage (Dominique Louis
), emerges with sacks of money.
As Mr. Incredible and the French-speaking Voyage face off, they are interrupted by Buddy, displaying rocket boots that he proudly announces to have invented himself. Despite Buddy's eagerness to help, Mr. Incredible tells him to go home. Adding insult to injury, Voyage criticizes Buddy's ridiculous outfit before placing a small bomb on the boy's cape as he leaves to get back-up. Mr. Incredible is forced to drop Voyage and grabs onto Buddy as he takes off, removing the bomb and dropping himself onto an elevated train track. The bomb detonates and destroys part of the track as a train approaches. Mr. Incredible uses his strength to stop the train just in time and later advises responding officers to Voyage's last location. He tells them to send Buddy home before he excuses himself, seeing as he's now late for his event. He hurries to the town church where he de-masks into his alter ego, Robert Parr, greets his friend Lucius Best (alter ego of Frozone), and walks down the aisle to marry Helen (Elastigirl). At the altar, he promises to be more than just Mr. Incredible to his new wife as they are wed in front of an ensemble of witnesses. Unfortunately, their bliss is short-lived as a series of news reports announce (with Teddy Newton
) that, in the face of one lawsuit after another involving civilian injuries and collateral damage, Mr. Incredible and other superheroes alike are forced to hang up their suits and assume their secret identities permanently.
The Superhero Relocation Program is created to provide ex-superheroes with new jobs and homes and amnesty for past actions. Robert is relocated to the suburbs and, 15 years later, is working a cubicle job in insurance under Gilbert Huph (Wallace Shawn
) who is as strict as he is short. Despite his monotonous work, Robert still tries to help people, including Mrs. Hogenson (Jean Sincere
), by showing them loopholes in the system to file their claims. Meanwhile, Helen goes to pick up their 9 year-old son, Dash (Spencer Fox
), from the principal's office at his school. His teacher, Bernie (Lou Romano
), insists that he knows Dash is responsible for a series of humiliating spats during class and presents a video that he claims shows Dash placing a tack on his chair during class, but moving too fast for the camera to see. Unconvinced, the principal (Wayne Canney
) dismisses Dash and Helen, much to Bernie's outrage. On the way home, Dash pleads with his mother to be allowed to play sports as an outlet for his super-speed powers but Helen refuses to give him that kind of temptation, repeating that they must try and live normal lives. She then picks up daughter Violet (Sarah Vowell
) from junior high. Violet has a crush on schoolmate Tony (Michael Bird
) but is too shy to speak to him and uses her invisibility powers to that advantage.
Robert returns home, severely disgruntled, and barely manages to restrain his frustration when he slips on a skateboard in the driveway and disfigures his car door. He lifts the car in the air right in front of a boy on a tricycle who remains stunned as Robert calmly lowers the car and walks inside. He joins his family for dinner but seems distant until Helen mentions Dash's sprint in school. While Dash and Violet begin a physical argument, much to baby Jack-Jack's (Eli Fucile
and Maeve Andrews
) entertainment, Robert goes into the kitchen and notices in the paper that an advocate for superhero rights and fellow super, Gazerbeam, has gone missing. As he returns to the dining room and attempts to quell his family's arguing, Lucius comes knocking and invites Robert out for a night of bowling.
In reality, they drive to an alley where they use a police scanner to find local disturbances as a woman with white hair monitors them from nearby. While Lucius proposes that they actually go bowling, Robert picks up a report of a fire. The white-haired woman follows them to an apartment consumed by flames where the ex-heroes, donning masks, manage to find everyone trapped inside. When Lucius is dehydrated to the point of being unable to create ice, Robert plows through an outside wall and into the building next door as the apartment comes crashing down. However, they find that they've landed inside a jewelry store and set off the alarms. A police rookie, already on site, holds Robert and Lucius at gunpoint, thinking them to be robbers, before Lucius grabs a quick drink of water and freezes the man on the spot. The other officers arrive just after Robert and Lucius make their getaway. As she watches, the white-haired woman speaks into a com-link that 'this is the one he's been looking for'.
Robert returns home where Helen is none too pleased to find what he's been doing with his time. They have a brief argument about Robert's wasteful reminiscing about the past until Violet and Dash appear, having been woken by the commotion. The following morning, Huph calls Robert to his office and confronts him on the fact that all his customers know the in-and-outs of the system. Robert listens with a grain of salt until he notices a man in a nearby alley getting mugged. His sense of justice still firmly intact, Robert goes to leave when Huph stops him, threatening his job. Robert watches helplessly as the mugger escapes and, with a snide comment of indifference from Huph, finally snaps. He grabs Huph by the neck and tosses him through multiple office walls. In the hospital, Robert meets with Rick Dicker (Bud Luckey
), his agent from the relocation program who explains that Robert can't keep trying to be the hero; it costs too much money to wipe memories and fill out all the necessary paperwork. Robert returns home dejected and can't bring himself to tell Helen he just lost his job. As he tosses the contents of his briefcase into the garbage in his office, he finds an unusual package stuffed within. He opens it and a scanner deems the room secure before a video message plays. The woman with white-hair, having infiltrated Robert's place of work to deliver the message, introduces herself as Mirage (Elizabeth Peña
) and tells Robert that 'they' know who he is. She offers him a job with a hefty payout and with the opportunity to give Robert a chance to return to superhero work before the message self destructs, causing the sprinkler system in the house to go off. Drying out books later, Robert tells Helen that he's been promoted and will be going on a business trip for a few days.
He calls Mirage and is picked up before being flown over a tropical island where Mirage's employer is based. She briefs Mr. Incredible on the mission: a robot invented by her employer has become self-aware and is now wreaking havoc on the island, threatening its facilities. Mr. Incredible is stuffed into an escape pod, with difficulty due to his girth, from the jet and dropped into a section of the island where the robot was last seen. He runs through the jungle, clearly out of shape, and finally comes across the rogue robot. The battle proves challenging since the robot learns from everything he does until they fall into the crater of the island's volcano. Mr. Incredible tricks the robot into destroying itself by removing its head and hiding in its body, sitting comfortably as it pierces its armor with its own claws. Mirage and her employer watche from a monitor via camera bird and Mr. Incredible is invited to dinner. He tells Mirage he usually likes to know who he works for, but seems satisfied regardless.
Robert returns home, with a hefty pay, and begins to change his outlook on his life. He pays more attention to his family, bequeaths his wife with gifts, and starts working out to attain a slimmer physique. Before his next assignment, Robert notices a tear in his old supersuit and pays a visit to Edna E Mode (Brad Bird
), former designer of the superheroes, now working with fashion models she calls 'skinny brats'. Intrigued by Robert's request for a patch-up, she offers to make him a new suit altogether.
When Mirage calls Mr. Incredible for his next mission, Helen checks the phone and becomes immediately suspicious that he is being unfaithful. She attempts to play this off and tells Robert how much she loves him before he leaves for his next 'conference'. He takes a private jet to the island where Mirage escorts him to his room, giving him instructions on where he is to go to be debriefed. He makes it to the conference room on time but finds no one there. Suddenly, the end of the room opens up and a larger version of the robot he battled before attacks. Despite Mr. Incredible's improvements in strength, the robot easily overpowers him and that's when his employer arrives on the scene, wearing rocket boots. The caped man reveals himself to be a grown Buddy, now realized as Syndrome, Mr. Incredible's arch nemesis. He explains that he was devastated after being denied the opportunity to become a hero but, despite having no superpowers, was able to use his dangerous intelligence to invent weapons to profit with, saving the best ones for himself to use for his revenge scheme against Mr. Incredible. Caught monologuing, Syndrome uses a laser invention in his glove to freeze Mr. Incredible and toss him into a nearby river. Mr. Incredible is able to escape by diving off the waterfall and swimming into an underwater cave as Syndrome drops a small bomb in after him. The explosion sends him into a subterranean cavern where he discovers the skeleton of Gazerbeam, still looking at a cryptic word he carved into the cave's wall before dying.
Meanwhile, Helen, while vacuuming Robert's office, discovers the patch job in his old supersuit. Suspicious, she calls the only person she knows would have done such a job; Edna. Edna invites a confused Helen over to see the 'new suits' and shows her a series of outfits she's designed for every member of the family. Helen is shocked to see matching suits for everyone, including the baby, and confronts Edna about what Robert is really doing.
Back on the island, Mr. Incredible manages to break in to Syndrome's base, taking out a number of guards in the process. He locates a master room behind a wall of flowing lava and, remembering the key word he saw in the cave, hacks into the database. He discovers, to his horror, that Syndrome has been luring ex-supers to the island with the promise of coming out of retirement only to pit them against his robotic inventions, wiping them out one by one. Mr. Incredible is relieved to see that Elastigirl's whereabouts remain unknown but finds that Syndrome is planning, with his latest robot, to attack the metropolis in less than 24 hours.
Edna gives an anxious Helen a remote GPS which can track the location of any suit wearer. Helen activates the remote, pinpointing Mr. Incredible's location but simultaneously sending out a transmission which breaks his cover. Immediately, a slew of guns along the walls fire balls of a heavy, sticky substance which expands on impact. The collective weight of the material weighs Mr. Incredible down and he is captured.
Devastated to have her fears confirmed, Helen breaks down until Edna demands that she pull herself together and go after her husband; to remind him of who she is as well. Helen takes the suits home and begins packing for her trip, trying unsuccessfully to keep the suits away from curious Dash and Violet. She pushes them out of the room, telling Violet that she's going to collect their father and should be back that night, before calling up an old pilot friend for a special favor. Snogg lends her a jet and, while en route, Helen attempts to make contact with the island. Disheartened to receive no response, she puts the plane on autopilot and goes to change into her supersuit.
Meanwhile, Syndrome confronts Mr. Incredible in the detention room. Restrained and held up by an electrical device, Mr. Incredible is helpless as Syndrome demands to know who he contacted when the transmission went through since a government plane is now requesting permission to land on the island. Syndrome plays the message and Mr. Incredible recognizes the voice as Helen's. Noticing his familiarity, Syndrome sends a 'greeting' of SAM missiles.
Back on the plane, Elastigirl finds that Violet and Dash have stowed away, wearing their supersuits. Despite their rash decision, Violet amends that she was able to get a babysitter (named Kari (Bret 'Brook' Parker
) who is featured with Jack-Jack in their own short) for Jack-Jack who, Elastigirl finds over the phone, turns out to be suitably qualified despite her neuroticism. The call is cut short, however, when she notices the plane has been targeted. She immediately takes evasive action, requesting disengagement from the tower. She soon becomes desperate and demands that Violet place a shield around the plane and shouts to the tower that there are children aboard. Mr. Incredible pleads with Syndrome to call off the missiles but the plane is destroyed and crashes into the sea. Mirage is visibly shaken when she confirms the crash and pushes Syndrome out of the way when Mr. Incredible lunges at him in fury. She is grabbed instead and Mr. Incredible demands that Syndrome let him go or she will be crushed. Syndrome sees through his bluff and scoffs at Mr. Incredible who, knowing he could never harm anyone, releases Mirage and breaks down as they leave. Syndrome calls him weak over his shoulder.
Elastigirl and the children, however, survive the attack. With Violet unable to produce a shield, Elastigirl created a ball around them with her flexible body and formed a parachute to land safely in the water. They follow the smoke trail of the missiles to the island with Elastigirl using her body as a makeshift raft while Dash speeds them along like a motor. They make land by nightfall and take residence in a cave. Elastigirl comforts her children, gives them masks to wear, and tells them to take care of each other while she goes to find their father. Should they run into trouble, Elastigirl goes back on her previous rules and tells them to use their powers to the best of their abilities. Violet tries to apologize for her failure on the plane but is consoled and advised not to think and not to worry. Elastigirl infiltrates Syndrome's facility, discovering a hangar with a rocket inside being fitted with the robot and locating Mr. Incredible's whereabouts within the detainment unit. Though a little rusty, Elastigirl proves a formidable enemy to Syndrome's guards.
As Violet practices her shield powers, Dash explores the cave and finds a separate tunnel within made of concrete. Before he can go further, Syndrome's rocket is launched and the children are barely able to escape the cave and the wall of fire running through it from the exhaust. Above the atmosphere, the rocket breaks apart and the robot, fitted to an alien-like ship, approaches the metropolis. At dawn, Violet and Dash wake up to see a talking bird which recognizes them as intruders. The alarms are set off and a small army of guards intersect and attack them once they find that they're supers. Dash runs off while Violet uses her invisibility (complete with her custom suit) to evade capture. As he runs from the guards piloting blade flyers, Dash is thrilled to find that he's fast enough to run on water. One by one, the pilots crash into obstacles or each other in their pursuit.
Meanwhile, having a change of heart due to Syndrome's indifference to her, Mirage returns to the detainment unit and releases Mr. Incredible, telling him that his family is alive and on the island. Relieved, Mr. Incredible hugs her just as Elastigirl walks in on the apparent romance. She quickly punches Mirage cold before Mr. Incredible pulls her in for an embrace. They then escape the facility together after Mirage tells them that their children have activated the security team. During the fighting, Violet discovers the potential of her powers and she and Dash are, eventually, reunited with their parents in the jungle. All together, they fight against Syndrome's thugs until they are captured, frozen by Syndrome's laser device. The family watches in horror from detainment as Syndrome gushes at the devastation the robot is wreaking over the city. He tells them that he plans to swoop in at the last minute and, using a remote on his wrist to deactivate the robot, save the day. Mr. Incredible is disgusted by Syndrome's plan at pretending to be a hero. Syndrome scoffs at him and says that he will be the only superhero left and, when he's old and had his fun, he'll sell his inventions so that everyone can be super...and when everyone is super, no one will be.
Meanwhile, in his apartment in the city, Lucius is preparing for a romantic evening out with his wife, Honey (Kimberly Adair Clark
), until he notices the robot rampaging through town. He back tracks to get his suit which he finds missing from its unit and banters with Honey over its location. She tells him that she put it away as he yells that he needs it for the greater good but she argues her plans, saying that she is the 'greatest good he'll ever get'.
Back on the island, Violet manages to use her powers to escape and frees her family. They make their way to the hangar where they discover a way, with Mirage's help, to reach the city in time. They fashion a Winnebago to a second rocket and drop in on the city as Syndrome appears and does battle with the robot. However, thanks to the robot's advanced learning technology, it blasts the remote off Syndrome's arm and knocks him into a nearby building, incapacitating him. Mr. Incredible goes in to duke it out and Elastigirl and the children tell him that they intend to help, despite his pleas otherwise; he couldn't bear to lose them a second time or risk them getting injured. Frozone arrives and, as a team, they work to take out the robot. Mr. Incredible finds Syndrome's remote and, through trial and error, they figure out a way to defeat the robot. Using a detached bit of the robot's arm, and remembering his first battle, Mr. Incredible launches it straight through the robot's core, effectively destroying it. The heroes are greeted by the grateful public with applause as Syndrome watches, defeated.
The family is taken home by Mr. Dicker and Elastigirl listens to a series of voice messages left for her by a very frantic Kari, explaining that their baby has 'special needs'. When Kari mentions the arrival of a replacement babysitter, Elastigirl says she didn't hire one and they rush into the home to find Syndrome holding Jack-Jack. He freezes the family and explains that, since Mr. Incredible took his future away, he'll return the favor by raising Jack-Jack to be his own sidekick. He blasts the roof and makes an escape for his hovering jet as Jack-Jack cries for his family, helpless on the ground. However, Jack-Jack becomes angry and shows Syndrome his abilities to shape-shift into almost anything, from turning his entire body into metal, fire, and then transforming into a demonic-looking monster that tries to throttle him. Syndrome drops Jack-Jack and Mr. Incredible throws Elastigirl into the air to catch him. She parachutes them down as Mr. Incredible then takes out Syndrome by throwing his car into the jet's engines. Echoing an earlier warning by Edna to Mr. Incredible over her distaste for capes, Syndrome is sucked into one of the engines and the jet explodes, landing in a fiery mess onto the Parr home. However, the family is saved by Violet's quick thinking and a safety shield.
The Parr family returns to normal life and attend a track meet together for Dash, happy to participate in sports. The family shouts encouragement, and tells him to hold back a bit to the confusion of other parents, as he runs and eventually comes in second place. Violet secures a date with Tony and the family celebrates together outside the track just as a large drill emerges from beneath the city streets. A new villain dubbed the Underminer (John Ratzenberger
) 'declares war on peace and happiness' as the Parr family, the Incredibles, put their masks on.