This issue serves as the conclusion to the "New Avengers" arc, where Spider-Man and his teammates confront the threat of Hydra. After preventing Hydra's missile attack, Spider-Man is rescued mid-air by Iron Man. Back at Stark Tower, Tony Stark conducts tests on Peter Parker and discovers unusual anomalies, hinting at deeper changes within Spider-Man. This sets the stage for the upcoming storyline, "The Other: Evolve or Die".

Peter disarms the missile, but he's riding it over the ocean at the time. Thankfully, Iron Man is on hand to bring him back in. Once he recovers, he starts to get adjusted to life in the tower again, in spite of a few surprises.

This issue is collected in The Amazing Spider-Man by J. Michael Straczynski Omnibus Vol. 1, which compiles issues #515–545 and related stories.