The film opens with Rick Dicker (Jonathan Banks) interviewing Tony Rydinger (Michael Bird). Tony had just asked out Violet Parr (Sarah Vowell), only for the Underminer (John Ratzenberger) to attack the city of Metroville. As Tony took cover, he noticed The Incredibles - Bob/Mr. Incredible (Craig T. Nelson), Helen/Elastigirl (Holly Hunter), Violet, Dash (Huck Milner), and Jack-Jack - about to spring into action, and he saw Violet take off her mask in a huff after being told to watch Jack-Jack. Dicker then erases Tony's memory.
We cut back to the battle with the Underminer as Bob tries to stop the villain from drilling any further into the city. Joining the fight is Lucius Best/Frozone (Samuel L. Jackson). Violet tries to leave Jack-Jack with Dash, but they keep pawning the baby off on one another as they race to help their parents. Bob catches up to the Underminer as he robs the Metroville Bank, leading to them fighting. The Incredibles stop the drill from hitting the town hall, but they are caught and are taken into custody. The cops chew out the Supers for casing damage and letting the Underminer escape.
The family is being taken back to their motel by Dicker, who informs them that the Supers Relocation Program is officially shut down because of the incident. Dicker tells Bob that the family can stay at the motel for another two weeks, and they're on their own after that. They later have dinner where Bob and Helen have to explain to the kids that even though they enjoyed fighting crime as a family, it's still illegal for Supers to be doing their jobs in public. Lucius then comes over as Bob and Helen are talking outside, and he tells them about a man he encountered during the Underminer battle, stating that he wants to meet the three of them together and that they should show up in their original superhero costumes.
Bob, Helen, and Lucius arrive at DevTech, a company owned by Winston Deavor (Bob Odenkirk), a huge fan of Supers. They are joined by Winston's sister Evelyn (Catherine Keener). Winston explains that their father loved Supers as well, even having a direct line to heroes like Gazerbeam and Fironic. However, after the Supers had to go into hiding, a break-in occurred at their house, and when their father couldn't reach either hero, he was murdered by the criminals, and their mother would pass away months later from heartbreak. Because of this, Winston wants Supers to come back into the spotlight and have the public's perception on them be changed. Evelyn has designed cameras on the Supers' suits to monitor their activities, and the Deavors want Elastigirl to be the face of their movement since she has a better track record with not causing so much destruction during her heroics, to Bob's disappointment.
At home, Bob and Helen discuss the mission, with the potential risks involving breaking the law and Helen having to leave her family. Bob then convinces Helen to go through with it so that their kids may be able to have the opportunity to save lives themselves soon enough. Helen then calls Winston and accepts the mission.
Winston moves the family into one of his houses and sets Helen up with a motorcycle to go on her mission, leaving Bob to take care of the kids, to his dismay. Helen learns of a potential threat as a new bullet train is being unveiled. Sure enough, the train goes in reverse, and Helen heads off as Elastigirl to save the passengers. She makes it onto the train and discovers that the conductor is under some kind of trance. Helen separates the train cars and manages to stop it from falling off the tracks. When Helen tries to talk to the conductor, he snaps out of his trance, and a message appears on the screen saying "Welcome back, Elastigirl - The Screenslaver".
Bob gets a call from Helen, who is excited about her accomplishment, though Bob is both proud and annoyed since he wishes it were him getting the glory. He also has a hard time adjusting to parenting on his own, as Dash needs help with complicated math homework, while Violet is upset because Tony forgot about his date with her. He also tries to get Jack-Jack to fall asleep, but after Bob passes out, Jack-Jack sees a raccoon outside going through the garbage and sees it as an intruder. Jack-Jack utilizes one of his many powers by phasing through the glass before engaging in a brawl with the raccoon. He catches fire, shoots laser beams from his eyes, and morphs into a monster before scaring the raccoon away, and Bob comes out to find him, excited that Jack-Jack has powers. Later on, he decides to familiarize himself with Dash's schoolwork to help him out.
Helen goes on a talk show with host Chad Bentley (Adam Gates). Before going on camera, she meets Ambassador Selick (Isabella Rossellini), who expresses her admiration for Elastigirl. As the interview commences, Chad falls under a trance, as does most of the crew. Helen runs out to the choppers that are escorting the Ambassador, and she realizes this is the work of the Screenslaver. She makes her way into the choppers and saves the Ambassador's crew before saving Selick herself as the chopper crashes and burns.
At school, Violet tries to talk to Tony, thinking he stood her up because he got freaked out when he saw her in her suit, but he doesn't actually remember her at all. When she mentions this to Bob, he accidentally blurts out that Dicker erased Tony's memory of her. Violet gets angry and renounces superheroism. Bob calls Dicker to see what he knows about Tony to fix things, and Dicker mentions a restaurant Tony's parents own where he works as a waiter. Bob takes the kids there to try and make it up to Violet, but when she sees he's the waiter, she freaks out and squirts water out her nose, humiliating herself and making her more upset at Bob.
The Deavors introduce Helen to a group of Supers from across the country, including Voyd (Sophia Bush), a young woman who is a huge fan of Elastigirl and has the power to create portals. There is also Reflux (Paul Eiding), an elderly Super who spews lava; Krushauer (Phil Lamarr), who can compact anything with his powers; and Brick, a huge mutant with brute strength. Helen then talks to Evelyn about Screenslaver, and she devises a plan to catch the villain by staging another interview and locking onto his signal.
Bob continues to get used to Jack-Jack's powers, though the kid proves to be a handful. Jack-Jack manages to teleport through dimensions and can be summoned with cookies, but when he is denied a cookie, he morphs into his monster form. Bob calls Lucius for help, and even he thinks Jack-Jack's powers are freaky. Meanwhile, Dash sees an auction going on from a guy who owns an old high-tech car of Mr. Incredible's, the Incredibile. Bob is annoyed that it's going on sale, as he still has the remote to control it, which he takes out and uses it to activate the car to scare the people on TV.
The interview is set up with Helen looking out on a nearby tower to catch Screenslaver. The villain hijacks the interview once again to taunt viewers, but Helen manages to track his location. She stretches herself across the city and goes to an apartment where she finds evidence of his plotting and tech, just before Screenslaver finds her. They fight, and Screenslaver runs after setting a bomb in the apartment. Helen catches him outside and unmasks him, revealing an ordinary pizza delivery guy who doesn't seem to have any memory of what he was doing. The apartment blows up, destroying the evidence.
Bob, having not been able to sleep after taking care of the kids, takes Jack-Jack to the home of Edna Mode (Brad Bird). While she is not used to being around kids, she becomes fascinated when she discovers one of Jack-Jack's powers is shapeshifting so that he can take on her appearance. Edna agrees to take care of Jack-Jack and help Bob.
While celebrating Helen's success in catching Screenslaver, she notices something odd in a picture of the villain, being that he had a screen with his own image shown from the camera in her own suit. She expresses this concern to Evelyn, just as they look at Screenslaver's mask. Helen pulls out a pair of mind-controlling goggles, and before she can come to a conclusion, Evelyn pushes the goggles onto Helen's face, revealing herself as the villain.
Bob visits Edna again to see that she has managed to keep Jack-Jack under control, and she has also made a suit to accommodate all of Jack-Jack's powers.
Helen wakes up tied to a chair where she is being super-cooled to prevent her from stretching. She realizes Evelyn was Screenslaver, but Evelyn says that she pre-recorded Screenslaver's messages and used the pizza guy as a pawn. Her reasoning is because she has a grudge against Supers due to her father's dependency on them instead of finding a hiding spot during the burglary, and she also can't stand the fact that Winston loves them so much as well. She wants Supers to remain illegal.
Under Evelyn's control, Helen calls Bob to inform him of some trouble. He calls Lucius to come by and take care of the kids while he goes to investigate, and once again, Lucius's wife Honey (Kimberly Adair Clark) is not happy about him running off. Not long after Bob leaves, Voyd and the other Supers arrive, all being controlled by Evelyn's goggles. Lucius arrives in time to use his freezing powers to fend them off, but they eventually catch him and put the goggles on him. Dash finds the Incredibile's remote and summons it to the house. He and Violet take Jack-Jack and head out of the house before the Supers can get them. They then decide they have to go help their parents, and the car is smart enough to help them out.
Bob finds Helen at DevTech, where she kisses him as a distraction to put the mind-control goggles on him. As Winston has organized an event on his yacht where the world leaders will lift the ban on the Supers, Evelyn is using this as an opportunity to turn the world against the Supers once and for all.
The kids miss the yacht as it sails away, but the Incredibile is able to ride on the water to catch up to it. They get on the yacht and try to find their parents, just as the hypnotized Supers find them and go after them. At the same time, the world leaders finish signing off on their deal, but as the event is televised, Evelyn uses Bob, Helen, and Lucius to come forward and state their supposed sinister intentions.
The kids find their parents as Evelyn makes the Supers steer the yacht toward the city. They manage to get the goggles off their parents and Lucius, who then have to fight the Supers team and get the goggles off them. After seeing that they are no longer under her control, Evelyn grabs Winston and tries to escape on her jet, but he refuses to join her and jumps back onto the ship. Helen goes after Evelyn with Voyd's help while Bob and the others try to stop the yacht from hitting the city. Voyd uses her portal powers to get Helen up to the jet, but Evelyn releases a gas to make Helen loopy before it kills her. Helen grabs a flare gun and blasts Evelyn out of the jet before she takes control of it and steers it into the ocean after ejecting herself. Helen grabs Evelyn, and Voyd manages to help them land back on the yacht. Bob and Lucius then manage to stop the yacht as Lucius creates a wave of snow to slow it down as it comes to a halt.
Evelyn is arrested, but Winston thanks Helen for saving her. The world leaders stand by their decision, and a judge lifts the ban on Supers for good.
Violet finds Tony at school and formally introduces herself. They go on a date, but with her whole family accompanying them to the movies. As they get to the theater, they see a couple of crooks speeding down the street after an apparent robbery. They drop Tony off as Violet promises to be back soon. The Incredibles then suit up and head off to fight crime as a family once again.
*CUT TO THE CHASE*
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After The Incredibles fail to catch The Underminer, the Supers Relocation Program is shut down. However, a rich tech developer named Winston Deavor recruits Helen/Elastigirl for a mission to change the public's perception on Supers. This leaves Bob/Mr. Incredible to stay at home and take care of Violet, Dash, and Jack-Jack, the latter whose powers are developing at a scary rate.
A villain calling himself The Screenslaver begins to terrorize the city by hacking into screens and putting people under a hypnotic trance. Helen catches Screenslaver, who turns out to just be a pizza delivery guy. It turns out that Screenslaver was just a pawn set up by Winston's sister Evelyn, who has a grudge against Supers because of her brother and late father's dependency on them, which led to her father's murder after he tried to contact Supers during a burglary. Evelyn wants Supers to remain illegal, and she uses mind-controlling goggles to put the Supers under a trance to have the public turn against them.
The kids race to save their parents, as well as another team of hypnotized Supers. They destroy the mind control goggles, but Evelyn has made it so that the yacht that they are on will ram into the city. Helen catches Evelyn before she can escape, and Bob, Lucius/Frozone, and the other Supers manage to stop the yacht from destroying the city. Evelyn is then arrested, and the Supers are allowed to come out of hiding once more.
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