A plane crash turns Norman Osborn back into the Green Goblin, who plans to turn the entire city into goblins.
Iceman and Firestar attend an X-Men reunion featuring Cyclops, Angel, and its latest members Storm and Wolverine (who oddly speaks with an Australian accent). Firestar recalls her origins (cameos by Magneto and a Sentinel). After that, the Juggernaut crashes the party in an effort to destroy his stepbrother Professor X.
After the Spider-Friends thwart the Scorpion, a chemical scientist named Zoltan Amadeus recreates Spider-Man's powers with a spider serum. He frames Spider-Man for his crimes. (Daredevil (Matt Murdock) guest stars as Spider-Man's lawyer). When Spider-Man ends up on Rikers Island, the Scorpion stages a jailbreak to take out Spider-Man, but is defeated. After Zoltan mutates into the Arachnoid, Iceman and Firestar cleared Spider-Man's name and are given the antidote to return Zoltan to normal.
Spidey falls in love with a stranded girl from the future, a girl named Ariel, whose spaceship has been stolen by Doctor Octopus. After Doctor Octopus is defeated, Iceman and Firestar learn that Ariel and her brother, Bartow are sick. In the hospital, it is revealed that they lack immune systems. Spider-man helps them return to the future, but Ariel's and Bartow's father returns Spider-man to the present because he carries germs from "Old Earth."
Buzz Mason of S.H.I.E.L.D. hires the Spider-Friends to stop a mutant named Lightwave, who has the power to control and manipulate light energy. She turns out to be Iceman's half-sister, Aurora Dante (who was not mentioned in "The Origin of Ice Man"). Though it is said that she has turned traitor and is targeting the GuardStar satellite, someone is actually mind-controlling her.