Three months following Syndrome’s defeat in the previous film, the Parr family – Bob, Helen, Dash, Violet and Jack-Jack – continue operating under their superhero identity, the Incredibles. When their attempt to stop the Underminer from robbing Metroville Bank failed, the authorities become concerned over the level of damage caused by the incident. Rick Dicker informs the Parr family that his department’s “Super Relocation” program is being shut down, forcing Supers across the world to permanently adhere to their secret identities, and he relocates the family to a motel as that is all he can do for them. Soon thereafter, Bob and Helen, along with family friend Lucius Best – the superhero Frozone, are contacted by Winston Deavor, a superhero fan, telecommunications tycoon, and owner of DEVTECH. Winston and his sister Evelyn Deavor, the genius inventor behind DEVTECH technology, propose a publicity stunt to regain the public’s support and trust in Supers.
Helen Parr is selected to be the first to undertake the stunt by openly fighting crime in New Urbem, under her old identity Elastigirl. As part of the plan, Winston provides the family with a new home and Bob offers to take care of the kids while Helen is away on her mission. Bob struggles at first but gradually settles into the role of a stay-at-home parent. He is delighted at the discovery that Jack-Jack has various super powers, but has a hard time trying to manage the baby’s abilities. Seeking help, Bob takes Jack-Jack to Edna Mode, a family friend and famous superhero-costume designer, who is fascinated with the baby’s powers. Meanwhile on her mission, Helen confronts the Screenslaver – a mysterious villain who hijacks screens in order to project hypnotic images that can brainwash people.
After rescuing a foreign ambassador in an attack by the Screenslaver, Helen tracks down and manages to capture the villain, who is only a pizza delivery man and has no recollection of what he did. While attending a celebration of the Screenslaver’s defeat at DEVTECH, Helen further investigates and realizes that the man was actually being controlled by hypno-screens within his goggles. Before Helen can alert anyone, Evelyn Deavor overpowers and forces Screenslaver’s goggles onto her. Evelyn reveals herself to be the mastermind behind the Screenslaver. Seeing Supers as a threat to humanity’s independence, she sought to undermine her brother’s mission and plans to use the superheroes to cause a catastrophe that makes it impossible for them to ever be legalized again. Evelyn uses Helen to lure Bob into a trap and uses other mind-controlled Supers to get the Parr children. Lucius arrives to protect the kids but is overpowered. Bob and Lucius are then placed under Evelyn’s control with the hypnotic glasses.
Violet, Dash, and Jack-Jack are able to escape and, with the help of the Incredimobile, they flee the house and locate the Deavors’ ship. On board, the mind-controlled Helen, Bob and Lucius recite a vindictive manifesto on air to paint themselves – and Supers in general – as a public threat before they are freed from Evelyn’s control by the children when Jack-Jack inadvertently frees his mother and displays other powers. Winston frees the other guests on the ship from Evelyn’s hypnosis by destroying the giant screen projecting hypnotic images. A battle ensues between the Supers, threatening to crash the ship into New Urbem. However, Bob, Lucius and the kids manage to slow the ship down before it can destroy the city. Evelyn tries to escape in a getaway jet attached to the ship but is eventually stopped and captured by Helen. Following the incident, Evelyn is arrested, Winston apologizes to Helen for being ignorant of Evelyn’s plan, and the Supers Relocation Program is reinstated, making Supers legal once again.