After been threatened by Adrian Toomes, Peter left homecoming to stop him from selling illegal weapons. Peter tells Ned to track him down and help get to Toomes after been confronted by the Shocker. When Spider-Man find him at his lair Toomes tries to justify his actions in which Spider-Man refuse to listen. Toomes summoned his Exo-Suit break the support beams around his lair, trapping Spider-Man under a pile of rubble and leaving him to suffocate. With Parker seemingly being crushed to death as his hideout fell apart around him, Toomes stepped outside and donned his Vulture Wings which had been upgraded by the Tinkerer. Encouraged by this realization, Spider-Man regained his resolve and began to painfully push the rubble off of him. Finally, he broke free of his entrapment and determinedly pursued Vulture.
Spider-Man managed to find Vulture. He webbed on to him as he flown toward the Stark Cargo Plane. Unaware of his presence, Vulture continued his hijacking. Crawling on the plane, Spider-Man attempted to remove Vulture's Wings that were covering the hole he made. It wasn't long before Vulture learned about his presence and another fierce fight happened in the sky.
Lacking his tech suit's advanced capabilities, Spider-Man could only improvise and dodged Vulture's relentless attacks. Their fight resulted in extensive damage to the cargo plane. When Spider-Man realized that the plane was about to crash into New York City, he used his Web-Shooters and strength to change the crashing to the beach of Coney Island instead. He succeeded and the plane crashed into the beach.
Exhausted and injured, Spider-Man was forced to take off his mask to breath. Without the mask, his senses overwhelmed him and allowed Vulture take him by surprise. Despite the damage on his adversary's suit, Vulture maintained the advantage and brutally attacked Spider-Man.
Despite Spider-Man best effort to defend himself, already exhausted, unable to focus and no nearby tall buildings to web onto, Vulture heavily injured him. Holding him up with his Exo-Suit Wings, Vulture was about to kill him when he spotted a nearby crate filled with Stark Industries' Arc Reactors. He then left Spider-Man on the ground and went to grab it instead. Spider-Man noticed that Vulture's wings were about to explode and tried to save him.
Finally, Vulture's wings exploded and crashed back down to the ground in flames. Spider-Man went into the flames and managed to find and save Toomes. He then webbed him to the remaining cargo and watched from afar as the police went to arrest Toomes.
Days later, back at school, Peter noticed that Liz was leaving. When he confronted her, she explained that since Toomes was about to go on trial, she and her mother were moving to Oregon to avoid the burden placed on having to attend his trial. As a result, her role on the Academic Decathlon's team was replaced by fellow classmate Michelle Jones.
While witnessing Michelle's promotion, Peter got a text message from Happy Hogan, who told him to meet him at the school bathroom. Peter arrived there, where Happy revealed that Stark was waiting for him back at the new Avengers Building and took Peter there by car.
Upon arrival, Stark apologized for taking Peter's upgraded Spider-Man Suit, but congratulated him for dealing with Toomes. Stark then offered Peter a new Spider-Man Suit, intending on making Peter the latest Avenger. Despite Stark and Happy promising a new life as an Avenger and a slew of reporters ready to welcome him, Peter refused, believing that he was not yet ready. Unknown to Peter, Stark really had arranged for reporters and Pepper Potts to cover Spider-Man's induction into the Avengers. Pepper was disappointed that Peter had refused, but Stark made up for it by proposing to her.
Peter arrived back at his apartment, where he found that Stark had returned his upgraded Spider-Man Suit. Excited to return to street-level crime-fighting, he donned the suit, not realizing that Aunt May had witnessed him.