Set in a world where "supers", people gifted with superpowers and abilities, are commonplace, the film opens up with three superheroes, Mr. Incredible, Elastigirl and Frozone, being interviewed. They talk about the subject of what being a superhero means to them, such as the importance of a secret identity, the burden of always being vigilant to protect the world from one threat after another, and the importance of superhero individuality.
The film begins proper with Mr. Incredible (Robert Parr), a super with Super-Strength and Toughness, going about his day, helping people and fighting crime. Along the way, he comes across a super-fan named Buddy Pine who wants to be his sidekick, and exchanges flirtatious banter with Elastigirl (Helen Truax), a super with elasticity powers. After a quick exchange with his friend Frozone, a super with cryogenic powers, Mr. Incredible saves a man from committing suicide, but in the process of doing so walks into the middle of a robbery being carried out by Bomb Voyage, a French supervillain who uses explosives.
Much to Mr Incredible's ire, Buddy arrives on the scene soon afterwards, having flown there with rocket boots he invented. He again insists that he should be Mr. Incredible's sidekick, but Mr Incredible bluntly tells him to go home, not wanting the kid involved in his work. To prove his worth, Buddy goes to get the police, only for Bomb Voyage to stick a bomb to his cape as he leaves, forcing Mr. Incredible to release the supervillain and go after Buddy. He removes the bomb from Buddy's cape, but drops it on a set of monorail tracks, causing it to destroy a portion of the tracks as a train approaches. Mr. Incredible succeeds in stopping the train just in time before it crashes, and hands Buddy to the police for compromising his mission and ensuring Bomb Voyage's escape. He is then forced to leave in order to attend an important event, which turns out to be his and Elastigirl's wedding.
Soon after his wedding, Mr. Incredible is sued for damages by both the man who was attempting to commit suicide, and the passengers of the train who were injured in his stopping of it. His court losses cost the government millions, and lead the way for a raft of lawsuits against supers. The financial burden of the lawsuits and rising anti-super sentiment causes the government to ban supers altogether, instituting the Superhero Relocation Program to give supers new civilian identities to spare them from public scrutiny.
Fifteen years later, Robert and Helen Parr are mere civilians and have three children: Violet, Dash and Jack-Jack. Bob works for insurance company Insuricare where his mean boss Gilbert Huph berates him for helping customers get access to their insurance payments, a situation which frustrates the former super. Dash, resentful of not being able to publicly use his powers of Super-Speed, uses them to pull pranks on his teacher. At dinner, Dash teases Violet about her middle school crush Tony Rydinger, which a starts fight between them, but is broken up by the arrival of Lucius Best, Frozone's civilian identity. Bob leaves with Lucius, as they do every Wednesday night, to moonlight as vigilantes, but tell their wives they go bowling.
While listening to the police scanner, they intercept a report of a fire nearby and proceed to rescue the people inside before the building crumbles. The duo barges into a jewellery store next door and are cornered by a police officer. Lucius gets a drink from a water cooler which gives him just enough water to petrify the cop so that they can slip away undetected. The only person who sees them flee is a mysterious woman who was spying on them before they departed, and reports that Frozone, who she was spying on, was with Mr. Incredible, who her boss wants. When Bob gets home, Helen tells him off for doing clandestine superhero work, leading to a full-blown argument erupting; Helen doesn't approve of Bob risking the family getting uprooted, while Bob resents having to hide his abilities. Bob and Helen find the kids listening in on them, and assure them that everything is fine, telling them to go to bed.
The next day, Mr. Huph is angry about Bob helping customers find loopholes in their insurance contracts so they get their payments, thereby reducing profits for Insuricare. During their conversation, Bob notices a mugging going on outside, but Mr. Huph threatens to fire him if he goes to help. Bob angrily watches the mugger getting away and Mr. Huph's smug remark causes Bob to lose his temper and throw him through several walls, exposing his super strength and costing him his job. As Mr. Huph recovers at the hospital, Bob meets with Agent Rick Dicker, an old friend who operates the Super Relocation Program. Dicker is frustrated because Bob has blown his cover multiple times before. Every time, Dicker has had to come to his rescue by relocating his family, erase everybody's memory of the incident and repair whatever damage has been done, which is very expensive. Bob declines Dicker's offer to relocate his family since his family just settled into their current home, and bids Rick farewell.
After returning home, Bob finds a message from the mysterious woman spying on him and Lucius last night, revealing her name to be Mirage and her knowledge of his superhero identity. She offers Bob a job at a faraway island that pays triple his annual salary; in which he must neutralize, but not destroy a prototype robot gone rogue before it causes incalculable damage to itself and millions of dollars worth of equipment. After reminiscing about the glory days and covering it up with Helen as a business trip, he calls Mirage and accepts.
Bob travels to Nomanisan Island in a jet with Mirage. She explains to him that the robot is called an Omnidroid, which can solve any problem it is confronted with, and is now intelligent enough to wonder why it was taking orders, wreaking havoc in the dense jungle. Upon landing on the island, Mr. Incredible searches for the robot until he finds trees with slash marks in them and a giant X on the ground. The Omnidroid emerges through the trees right behind him and the fight ensues. He assumes victory, hurting his back in the process, when he tricks it into falling into a lava pit, but it rises from the lava unscathed. Seeing no other way to fight it, he tries to escape on a floating rock, but the Omnidroid catches him and tries to tear him in half. But all it does is realign his back and he tears off one of its claws. Mr. Incredible hides in its blind spot directly beneath it, and tears out one of its optical clusters and climbs inside of it. In trying to attack Mr. Incredible, it repeatedly skewers itself. Mr. Incredible emerges and tricks it into ripping out its own power source, destroying it. After the battle, a surveillance drone disguised as an island parrot reveals that Mirage and her boss have been watching, and Mr. Incredible has dinner with Mirage. Upon returning home, Bob finds the action and higher pay rejuvenating. He improves his relationship with his family and begins rigorous training to lose weight.
Discovering a tear in his suit from the battle with the Omnidroid, Mr Incredible visits another old friend, superhero costume designer Edna Mode. Instead of fixing the suit, Edna agrees to make him a brand-new suit before his next assignment and sends him on his way, while begrudgingly agreeing to fix the old suit for sentimental reasons. He also suggests giving the suit a cape, but Edna shoots his idea down, pointing out that several supers were killed when their capes got stuck in various objects. Back home, Helen spots a silver hair on Bob's business suit and eavesdrops on a secret call for him when Mirage summons him for a new assignment. Suspecting there may be someone else eyeing for her husband, Helen confronts Bob about who the call was from, and nervously wishes him love and luck on his "business trip". While vacuuming in Bob's private office, she notices the sewn-up tear where Edna fixed the old suit and calls her, and Edna tells her to visit.
Back on the island, Mr. Incredible makes his way into the conference room, allegedly to be briefed on his assignment. Instead however he is ambushed by the upgraded Omnidroid v.9. While trapped by the robot, he meets its creator, the technology-savvy supervillain Syndrome, who Bob recognizes as Buddy. Syndrome vowed revenge for being rejected, and as he brags about how he has won, Mr. Incredible throws a log at him, but Syndrome dodges it and traps Mr. Incredible using his zero-point energy. After throwing Mr. Incredible around in order to show his power over the superhero, Syndrome accidentally throws him over a waterfall and into a river. Syndrome sends a bomb to kill Mr. Incredible, and sends a probe to ensure that Mr. Incredible has been killed.
Mr. Incredible manages to avoid the explosion and, discovering the bones of former Super and friend Gazerbeam, fakes his death by hiding from the probe behind them. In the process, he discovers that Gazerbeam used his powers to inscribe "KRONOS" into a cave wall. Determined to discover Syndrome's plans, Mr. Incredible breaks back into his facility, finds a computer and, using "Kronos" as the password, discovers a plan to systematically eliminate Supers. Each super was pitted against increasingly advanced models of the Omnidroid, and if not terminated by one model, they would be terminated by the next one. He also discovers that, although Lucius' location is known, Helen's is not. As he browses the database further, he discovers that Operation Kronos' final stage is to unleash an Omnidroid on Metroville via rocket deployment.
Meanwhile, Helen has become suspicious of Bob having an affair. After discovering Bob's repaired suit, she visits Edna and learns that in a burst of creativity, she created suits for the entire Parr family, each outfitted with a tracking device. Edna questions if she knows where Bob is, so Helen calls Insuricare and they reveal he has been unemployed for 2 months. Helen activates the tracking device built into her husband's suit so she can find him. Just as he was about to leave the computer room and set about stopping Operation Kronos, Mr. Incredible's suit makes a beeping noise, leading to his capture.
Helen borrows a private plane to head for Nomanisan island, but Violet and Dash have stowed away wearing their own suits, leaving Jack-Jack with a babysitter. Syndrome interrogates Mr. Incredible about the transmission from a plane requesting permission to land, but Mr. Incredible is oblivious to the plane. When the transmission reveals it to be Helen's plane, Syndrome sends missiles towards it. Helen evades the first wave of missiles, but due to Violet not being able to produce a force field large enough to shield the plane, the plane is shot down, with Elastigirl shielding her kids and safely landing on the water with them. Mirage reports that the target was destroyed and its passengers presumed dead. Enraged, Mr. Incredible tries to force Syndrome into releasing him by threatening to kill Mirage. However, Syndrome smugly calls his bluff and leaves him crestfallen at the apparent loss of his family.
Helen, Violet and Dash reach the island and take refuge in a nearby cave. Before she departs to look for Bob, she tells Dash and Violet to use their powers to escape the bad guys, and she apologizes to Violet for what happened on the plane. Meanwhile, Mirage tells Syndrome that valuing life is not weakness, and angrily tells him to gamble his own life next time, before storming off, leaving him mystified. Elastigirl sneaks in, finding a rocket on her way to finding Mr. Incredible. Back in the cave, Violet practices with her force bubbles while Dash walks through the cave. Dash discovers that the inside of the cave ends with a huge metal tunnel. Syndrome initiates the launch command and the rocket blasts off, with the Omnidroid v.10 onboard. The cave Dash and Violet are in is an exhaust vent for the rocket's liftoff. and gets himself and Violet out just in time. Back inside the fortress, Elastigirl locates the control center for the containment unit's cellblock matrix and finds out exactly where Mr. Incredible is. Meanwhile, the rocket reaches optimum position and the glider carrying the Omnidroid is released and sent towards Metroville.
The next morning, Dash and Violet are in the jungle, waking up to a talking parrot, only to reveal itself as a security drone, and it signals a security alert. Meanwhile, Mirage releases Mr. Incredible after having her change of heart, and informs him of his family's survival. At the same time, Elastigirl arrives and races off with him to find their children. Dash and Violet are spotted and chased by a number of Syndrome's guards, but fend them off with their powers. Dash evades the guards using his super speed while Violet turns invisible to hide. Dash stops a guard from shooting Violet, then she returns the favour with a large force field. Dash runs inside the force field, mowing down several guards.
After reuniting with their parents, the family engages in a showdown with the guards, taking out several of them before being captured and imprisoned by Syndrome. The supervillain reveals his plan to the Incredibles: he will allow the Omnidroid to cause destruction in Metroville, and then show up to defeat it and "save" the city, causing the people to revere him as a hero. Bob is disgusted that in the end, Syndrome's plan boils down to him killing off real supers so that he can pretend to be one; utterly missing the point, Syndrome claims that even without powers he was enough of a 'hero' to defeat Mr Incredible, and declares that when he's old he'll render the term 'Super' useless by selling his gadgets to everybody. He departs for Metroville, leaving the Incredibles imprisoned on Nomanisan Island. After his departure, Mr. Incredible vents his grief about being the cause of all of this, claiming that he's been so afraid of being undervalued, he undervalued his own family. Violet uses her force field to sever her magnetic bonds, and frees the rest of the family, and with Mirage's help, they board a rocket bound for the city.
In Metroville, Syndrome "stops" the Omnidroid from harming anyone, much to the public's delight. However the Omnidroid, being a learning robot, identifies Syndrome's remote as being its control source, and fires it off his arm, then shoots at his rocket boots, sending him flying into a building and knocking him unconscious. While the robot is on a rampage, Lucius searches for his suit that was hidden by his wife Honey. The Incredibles arrive in Metroville, but Mr. Incredible orders everyone to stay behind, though Elastigirl objects, leading him to say that he doesn't want to lose his family again. Violet shields herself and Dash from the Omnidroid until it sits on the shield, rendering her unconscious. Mr. Incredible and Elastigirl get them to safety and team up with Lucius, now in his Frozone suit, to fight the Omnidroid.
Mr. Incredible finds the remove and throws it to Dash, who races to get it with the Omnidroid firing at him and trapping him amongst burning cars. Elastigirl slingshots a manhole cover and destroys the robot's laser, whilst Frozone rescues Dash. The robot then vaults itself into the air and nearly crushes Frozone and Dash, but he manages to freeze the air around them and cushions their fall. Violet obtains the remote while invisible and brings it back to the group. Remembering his battle with the Omnidroid v.8, Mr. Incredible concludes that the only thing that could penetrate it is itself. Elastigirl obtains the claw needed to pierce the robot. Mr. Incredible directs her to use the remote to release the powered-up claw, which pierces the Omnidroid and its power source. It falls mundanely into the river and explodes, and the city laud the Incredibles and Frozone as heroes. Syndrome awakens, only to discover his plan foiled, and is very angry that the Supers are being celebrated.
In a limousine on their way home, Dicker is proud of the Incredibles for defeating Syndrome. Syndrome's assets are frozen and a warrant is issued for his arrest, while everything regarding collateral damage will be handled personally. During the ride home, Elastigirl is listening to messages left by Kari, Jack Jack's babysitter, who appears to be very stressed, and arranged for a replacement. The replacement is Syndrome, who plans to kidnap and raise Jack-Jack as his sidekick to exact revenge on the family. As Syndrome flies to his manta jet, Jack Jack's superpowers manifest and he escapes from Syndrome in mid-air, to be saved by Elastigirl. When Syndrome announces that he will be back, Mr. Incredible throws his sports car at the manta jet and Syndrome is pushed backwards by the resulting explosion. Syndrome is killed when his cape sucks him into the jet turbine and the manta jet explodes. The Parrs' house is destroyed by the falling jet, but they are saved by Violet's force field.
Three months later, the Parrs are watching Dash racing at a track meet. Violet arranges a movie date with Tony and Dash finishes second to avoid suspicion. After the event, the family witness the arrival of a new villain named the Underminer and don their superhero masks, ready to face a new threat.
