In Ixtenco, Mexico, Nick Fury (Samuel L. Jackson) and Maria Hill (Cobie Smulders) delve into a mysterious storm, leading them to confront the formidable Earth Elemental. Enter Quentin Beck, also known as Mysterio (Jake Gyllenhaal), a master of illusion who claims he is a superhero from an alternate reality, Earth-833. Meanwhile, back in New York City, the Midtown School of Science and Technology resumes for the school year, welcoming back students who had been affected by "the Blip"—a phenomenon that resurrected individuals after five years.
As the school plans an exciting two-week summer field trip to Europe for the academic decathlon team, Peter Parker (played by Tom Holland) grapples with his own troubles, particularly the loss of Tony Stark. Hoping to confess his feelings to MJ (played by Zendaya), Peter aims to navigate the trip without any superhero antics. His best friend, Ned Leeds (Jacob Batalon), encourages him to focus on enjoying their European adventure while keeping his feelings for MJ under wraps.
During a homeless fundraiser organized by his Aunt May ([Marisa Tomei]), Peter receives a cryptic warning from Happy Hogan ([Jon Favreau]), the head of security for Stark Industries, about an impending call from Fury. Attempting to escape from the overwhelming inquiries about Stark, Peter decides to ignore Fury's call.
As Peter and his friends board the flight to Europe, his desire to sit beside MJ falls apart when the teacher chaperoning the trip, Roger ([Martin Starr]), rearranges their seating. The other chaperone, Julius ([JB Smoove]), adds to the chaos. While Ned finds himself next to Betty ([Angourie Rice]), MJ ends up sitting next to Brad (Remy Hii), a popular student whom Peter perceives as a rival for MJ’s attention.
Their journey takes them to Venice, where the Water Elemental unleashes chaos. Enter Mysterio, who swiftly eradicates the creature while Peter does his best to mitigate the destruction. Peter dreams of giving MJ a Black Dahlia pendant atop the Eiffel Tower in Paris, hoping it will be the perfect moment to express his feelings.
Fury eventually meets with Peter, gifting him Stark's and providing him with high-tech glasses called E.D.I.T.H. (Even Dead, I'm The Hero), which offers immense power and intelligence. Taken to a hidden headquarters, Peter is introduced to Beck and Hill, who claim that four powerful Elementals have emerged from black holes, each representing fundamental elements. Beck laments the loss of his family and home, leading to Peter's internal struggle as he declines Fury's call to action, wishing to stay with his classmates.
Fury decides to steer the class trip off course to seek the Fire Elemental in Prague, not fully believing Peter is fit for the responsibility. Doubting himself, Peter tries to keep his friends out of danger while secretly longing for a normal life. The Fire Elemental attacks, and with Beck's help, they manage to vanquish it, protecting Ned and Betty in the process.
On a new quest to build a superhero team, Fury invites Peter and Beck to Berlin. Peter sees Beck as a potential successor to Stark and gifts him the E.D.I.T.H. glasses, believing that Stark wanted him to choose someone worthy. However, unbeknownst to Peter, Beck’s true character is revealed as he is a disgruntled ex-Stark employee using advanced technology to impersonate a hero.
As MJ uncovers Peter's secret, she discovers crucial evidence that unveils Beck as a fraud. Peter heads to Berlin, only to confront a series of illusions created by Beck, ultimately realizing he has been misled. After a grueling fight, Peter survives an attack by illusions and escapes a train, waking up in a jail cell in the Netherlands.
With the support of Hogan, Peter utilizes Stark's technology to create a new customized suit. Beck’s plans escalate as he orchestrates his greatest illusion yet that threatens MJ’s life and aims to erase any witnesses to his deception. In a tense showdown, Peter overcomes Beck's ruse, regains control of E.D.I.T.H., and defeats him in a dramatic conclusion.
Returning to New York City, Peter embarks on a blossoming romance with MJ. In a shocking mid-credits scene, J. Jonah Jameson (J.K. Simmons) blames Spider-Man for the recent chaos, broadcasting manipulated footage that tarnishes Peter's image and exposing his secrets. In a post-credits reveal, Talos and Soren are shown to have been impersonating Fury and Hill under the orders of the real Fury, who is operating from a Skrull spaceship.
