Spider-Man wants to recruit Cloak and Dagger as new warriors for his S.H.I.E.L.D. team. Complicating the matter, however, are Dormammu taking control of Cloak and Dr. Strange in an attempt to invade Earth, and Cloak and Dagger's own trust issues.

Now that the other young heroes have been assembled, Spider-Man must lead them into defending the Tri-Carrier from the Thunderbolts (consisting of Taskmaster, Vulture, and Cloak and Dagger) where they managed to spring Green Goblin, Doctor Octopus, Beetle, and Scorpion from their cells.

Arnim Zola resurfaces and starts replacing Spider-Man's fellow students with synthezoid versions of themselves.

Spider-Man faces the culmination of all Doc Ock's evil machinations when the new Sinister Six assaults the Web Warriors and S.H.I.E.L.D. Academy at the Triskelion.

When Doc Ock learns that the key to a device that will retrieve Hydra Island is at Aunt May's house, Spider-Man must fight to protect his family.

Spidey must track down Ock before he harms Aunt May.