In Ixtenco, Mexico, Nick Fury and Maria Hill investigate an unnatural storm and encounter the Earth Elemental. Quentin Beck, a super-powered man, arrives to fight the creature. In New York City, the Midtown School of Science and Technology restarts its academic year to accommodate the students who were among those resurrected in “the Blip” eight months earlier. The school organizes a two-week summer field trip to Europe, where Peter Parker, while still distraught over Tony Stark’s death, plans to confess his growing feelings for classmate MJ and avoid heroics. At a fundraiser for the homeless coordinated by his Aunt May, Parker is forewarned by Happy Hogan that he will be contacted by Fury, but he chooses to ignore the call. Parker leaves after being overwhelmed by questions about Stark.
Parker and his classmates travel to Venice, Italy. His classmate Brad emerges as a competitor for MJ’s affections. The Water Elemental strikes Venice and wreaks havoc on the city. Beck arrives and destroys the creature. Fury meets with Parker and gives him Stark’s glasses, which were meant for his successor. The glasses are equipped with the artificial intelligence E.D.I.T.H., which has access to all databases of Stark Industries and commands a large orbital weapons supply. Beck claims the Elementals killed his family and that he hails from a different reality, one among many in the Multiverse. Parker rejects Fury’s call to arms, opting to rejoin his class.
Fury covertly redirects the school trip’s itinerary to Prague instead of Paris, where the Fire Elemental is projected to strike. It appears at a carnival, but Beck, with Parker’s help, destroys it. Fury and Hill invite Parker and Beck to Berlin to discuss the formation of a new superhero team. Parker considers Beck worthy of being Stark’s successor and bequeaths him the E.D.I.T.H. glasses. Unbeknownst to him, Beck is revealed to be a former holographic-illusions specialist at Stark Industries who was fired for his unstable nature. He now leads a team of disgruntled ex-Stark employees, using advanced projector drones to simulate the Elemental attacks and masquerade as a hero.
MJ deduces Parker is Spider-Man. They discover that a piece of debris she retrieved during the carnival battle is a projector that presents a simulation of the Air Elemental, leading the two to realize Beck is a fraud. Parker travels to Berlin and meets with Fury. Realizing that he is in an illusion, Parker battles multiple illusions before Fury apparently subdues Beck. Fury forces Parker to reveal anyone he told of Beck’s deception before being revealed as another illusion. Ultimately hit by a train, a badly injured Parker falls unconscious in a train car.
Awakening in a jail cell in the Netherlands, Parker breaks out and contacts Hogan, who flies Parker to London and reveals a suit-manufacturing machine left behind by Stark, which Parker uses to synthesize a customized costume. In London, Beck uses E.D.I.T.H. to orchestrate his biggest illusion yet, a fusion of all four Elementals, using it as cover to kill MJ and any others to whom she might have revealed his secret. Parker disrupts the illusion, so Beck reveals the drones to attack him. Parker defeats Beck, regaining control of E.D.I.T.H. to call off the drone attacks. Beck dies from wounds sustained from misfired drone gunshots. An assistant of Beck’s escapes with data of the events. Parker returns to New York City and begins a relationship with MJ.
In a mid-credits scene, journalist J. Jonah Jameson of TheDailyBugle.net broadcasts doctored footage of the London incident, in which Beck incriminates Spider-Man for the drone attack and his death, before revealing Spider-Man’s secret identity. In a post-credits scene, the Skrulls Talos and Soren are revealed to have been masquerading as Fury and Hill the whole time, as directed by the real Fury, who is seen commanding a Skrull spaceship.