In 1987, Janet van Dyne shrinks between the molecules of a Soviet nuclear missile, disabling it but entering the microscopic Quantum Realm. Hank Pym raises their daughter Hope believing that Janet is dead.

In the present day, Scott Lang spends time with his daughter Cassie. Although he was arrested and imprisoned for helping Captain America during a skirmish between the Avengers in violation of the Sokovia Accords, Lang took a plea bargain and was allowed to return to the US. Lang was sentenced to two years under house arrest, with a twenty-year minimum prison sentence waiting if he leaves his home during his sentence or defies the Sokovia Accords again. As Pym and Hope had provided Lang with the technology he used against the Avengers, they were ruled to have also breached the Accords and a warrant for their arrest was issued forcing the two to go on the run while severing all contact with Lang.

Lang spends the next two years keeping himself busy various ways (including learning close-up magic), and also sets up a security company with his friends Luis, Dave and Kurt to allow them to earn an income. When he has just three days left until his release from house arrest, Lang has a dream where he relives one of Janet's memories of when Hope was a child. Despite not wanting to jeopardize his release, Lang contacts Pym on a phone he'd hidden away and briefly tells him what's happened, before deciding he sounds like an idiot, apologizing for all the trouble he landed on them and smashing the phone. That night, as Lang relaxes he notices something buzzing nearby before being suddenly knocked out. When he wakes up, Lang finds he has been kidnapped by Hope, leaving a decoy so as not to arouse suspicion from the FBI agent Jimmy Woo. Hope is clearly angry with Lang for using the Ant-Man suit and helping Captain America without telling her as well as forcing her and her father into hiding but tells Scott that his dream coincided with Pym briefly opening a quantum tunnel. Seeing the message as confirmation that Janet is alive, Pym and Hope work in their new lab (which Pym can shrink for whenever they need to move) to create a stable tunnel so Hope can take a vehicle into the Quantum Realm and retrieve Janet. Lang meets Pym who is also very bitter towards Scott for his actions but puts it aside for now as he and Hope decide Lang is their only hope of locating Janet's coordinates in the Quantum Realm.

Hope arranges to buy a part needed for the tunnel from the black market dealer Sonny Burch, however, Burch has realized the potential profit that can be earned from Pym and Hope's research and double-crosses them. Hope then reveals she has a shrinking suit of her own, one which can fly and has blasters, and uses it to fight Burch and his men off and retrieve the part. Before Hope can leave, however, she is attacked by a quantumly unstable masked woman, referred to as the Ghost. Lang tries to help fight off the Ghost and they keep hold of the part, but Ghost escapes with Pym's portable lab.

Pym reluctantly visits his estranged former partner Bill Foster who helps them locate the lab. The ghost restrains Lang, Hope, and Pym when they arrive, and reveals herself to be Ava Starr. Her father, Elihas Starr, another former partner of Pym's, accidentally killed himself and his wife during a quantum experiment that caused Ava's unstable state. Foster reveals that he has been helping Ava after the accident, who they plan to cure using Janet's quantum energy. Believing that this will kill Janet in the Quantum Realm, Pym refuses to help them and the trio manage to escape.

Opening a stable version of the tunnel this time, Pym and Hope are able to contact Janet who gives them a precise location to find her, but warns that they only have two hours before the unstable nature of the realm separates them for centuries. Burch learns their location from Lang's business partners Luis, Dave and Kurt, and informs a contact at the FBI. Luis warns Lang, who then confesses to Hope and Pym, which angers them and prompts them to sever ties with him again. Lang is forced to rush home before Woo can see him breaking his house arrest. This leaves Pym and Hope to be arrested, and for their lab to be taken by Burch. Back at home, Lang is convinced by Cassie to rescue Hope and Pym despite the risks, promising that she'll love him no matter what happens.

Lang is soon able to help Pym and Hope escape custody, and they steal the lab back from Burch. Lang and Hope distract Ava while Pym enters the quantum realm to retrieve Janet, but end up fighting Burch and his men allowing Ava to begin the process of taking Janet's energy. A car chase ensues across the streets of San Francisco, ending at Pier 39. Lang takes the lab and enlarges it, while Burch and his goons are apprehended.

During this, Pym encounters Janet in the Quantum Realm, and arrive safely from the Quantum Tunnel. Ava attempts to sabotage their return, but when Lang and Hope intervene, she is stopped. Janet voluntarily gifts some of her energy to Ava to stabilize her condition. Lang returns home once again, in time for a suspicious Woo to release him at the end of his house arrest. He then happily reunites with Cassie, while Hank restores the family home (which he had shrunk and was hiding) on the beach for him and Janet.

In a mid-credits scene, Lang ventures into the Quantum Realm to collect particles to help heal Ava, while monitored by Hank, Janet, and Hope. Although he is successful in harvesting the particles, Hope's countdown to bring him back suddenly cuts out. It is revealed that Hank, Janet, and Hope have all been turned to ash, leaving Lang trapped in the Quantum Realm.

In a post-credits scene, an oversized ant plays the drum kit in Lang's house while the television is broadcasting a state of emergency.