In Ixtenco, Mexico, Nick Fury and Maria Hill investigate an unnatural storm and encounter the Earth Elemental. Quentin Beck, a super-powered individual, arrives to defeat the creature. A week later, in New York City, the Midtown School of Science and Technology completes its academic year, which was restarted to accommodate the students who disappeared during the five-year period known as the Blip. They had reappeared unaged, thanks to the actions of the Avengers.[N 1] The school organizes a two-week summer field trip to Europe, where Peter Parker—still mourning the death of his mentor and father figure Tony Stark—plans to reveal to classmate MJ his attraction to her. Happy Hogan informs Parker that Fury intends to contact him, but Parker ignores Fury's phone call.
Parker and his classmates travel to Venice, Italy, where the Water Elemental attacks. Parker helps protect his classmates, while Beck arrives and destroys the creature. Fury meets with Parker and gives him Stark's glasses, which were meant for his successor. The glasses enable him to communicate with and take command of the artificial intelligence E.D.I.T.H., which has access to Stark Industries' databases and commands a large orbital weapons supply. Beck claims to hail from an alternate reality within the Multiverse, where the four Elementals killed his family and destroyed his civilization. He predicts that the Fire Elemental will appear in Prague. Parker declines Fury's invitation to join the fight and returns to his class trip.
Fury secretly changes the class's itinerary to divert the students to Prague. There Parker is forced to help fight the Fire Elemental to again protect his friends. Beck is able to destroy it with Parker's help. Fury and Hill invite Parker and Beck to Berlin to discuss the formation of a new superhero team, but Parker decides that Beck should go alone and transfers control of E.D.I.T.H. to him. In actuality, Beck is secretly 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; their goal was to gain control of E.D.I.T.H. They use the orbital weapons drones to increase the scale of their illusions.
MJ tells Parker she knows he is Spider-Man. They discover that a piece of debris she retrieved during the battle is a projector that shows part of the Air Elemental's attack, leading them to realize Beck is a fraud. Parker travels to Berlin to warn Fury, but "Fury" is actually one of Beck's illusions. Parker accidentally reveals that he told some of his friends about Beck's plan. Beck distracts him with illusions and maneuvers him into the path of a speeding train. Beck assumes he has been killed, but he is merely knocked unconscious. Parker contacts Hogan, who flies him to London, where his classmates are. Beck uses E.D.I.T.H. to orchestrate his biggest illusion yet, a fusion of all four Elementals, as a cover to kill Parker's friends. Parker is able to disrupt the illusions, so Beck attacks him with drones. Parker defeats Beck and takes back control of E.D.I.T.H. Beck dies from wounds sustained from misfired drone gunshots. One of Beck's assistants escapes with data from the drones. After returning to New York City, Parker begins a relationship with MJ.
In a mid-credits scene, J. Jonah Jameson of TheDailyBugle.net broadcasts doctored footage of the London incident in which Beck frames Spider-Man for the drone attack and his death, before exposing his secret identity to the world. In a post-credits scene, Fury and Hill are revealed to be the Skrulls Talos and Soren in disguise, under orders from the real Fury, who is seen commanding a Skrull spaceship.