Spider-Man accepts Nick Fury’s offer to become the Ultimate Spider-Man and meets his new allies of young heroes consisting of Nova, White Tiger, Power Man and Iron Fist. Meanwhile, Norman Osborn orders Doctor Octopus to send the Frightful Four to target Spider-Man. Spider-Man ends up having to get help from his new allies to fight off the Frightful Four.
After Spider-Man and Nova’s childish argument gets their team grounded, the young heroes browse S.H.I.E.L.D.'s database to find a supervillain they can defeat to impress Nick Fury. Unimpressed by lower-tier villains like Batroc the Leaper and Toad, they decide to take on Doctor Doom in Latveria. They successfully capture him but later realize they’ve been tricked into bringing a Doombot aboard the Helicarrier, leading to more trouble.
When Spider-Man meets his idol Iron Man, he receives a specialized gift: the Iron Spider suit. However, Spider-Man experiences difficulty learning how to use the suit and begins to neglect his teammates. Meanwhile, the heroes battle "The Living Laser", who takes advantage of Spider-Man's lack of experience using the new suit.
Venom resurfaces using Harry as his host yet again; this time Harry's neglecting father becomes his main target. While Norman Osborn does not want his potential secret weapon damaged, Spider-Man is confronted with the dilemma of either trying to help Harry on his own or putting his trust in his teammates, who have orders from Fury to finish Venom off.
When New York is plunged into a mystical sleep, Iron Fist and Spider-Man (who is at first highly sceptical of magic) seek the help of Doctor Strange. In order to break the spell, the three heroes must face their own worst fears in the face of the spell's initiator, the extradimensional entity known as Nightmare.
Spider-Man and his team are put on S.H.I.E.L.D. security detail to protect the all-too-critical-for-his-own-health J. Jonah Jameson from the Beetle, a prospect Spider-Man does not enjoy. Things do get personal when Spider-Man must also protect a highly determined Mary Jane, who is on her way to the Bugle for a job interview, from the high-tech villain.
When Phil Coulson wants the heroes to report to the S.H.I.E.L.D. ice base for winter survival training, Spider-Man and his team sneak off for a vacation on a deserted tropical island that Nova finds under "classy." However, they soon realize something is not right with the island and the Sandman will make sure they never leave.
Using a Norn Stone, Loki shrinks Spider-Man's team while looking for Thor. Nick Fury has Spider-Man's team placed in the Helicarrier's D.A.Y.C.A.R.E. area while S.H.I.E.L.D. continues to look for Thor. With Thor also having been shrunk, Spider-Man's team must find a way to help Thor fight Loki and the Destroyer Armor and return to normal size.
The Guardians of the Galaxy land on Earth to repair their ship at the same time Titus leads the Chitauri into targeting Nova's helmet. Now Spider-Man and Nova must work with the Guardians of the Galaxy to defeat Titus and the Chitauri. This episode was originally aired out of order to promote the Guardians of the Galaxy movie.
Spider-Man, the Avengers and the Agents of S.M.A.S.H. battle their greatest foes for the fate of the planet. Spider-Man is chosen to be part of the Collector's team and is partnered with Hulk and Iron Man against the Grandmaster's team of villains consisting of Kraven the Hunter, Molten Man and Wendigo King.
Spider-Man is partnered with Captain America, Red Hulk and Iron Fist in a game of capture the flag against Sandman, Blastaar and Ymir. Then Spider-Man is partnered with Power Man, Black Widow and Skaar against Doctor Octopus, Absorbing Man and Zzzax in a game of last team standing but things become a problem when the Grandmaster starts changing the environment of the game.
Peter Parker learns Doctor Octopus has teamed up with Arnim Zola and Hydra to attack the Tri-Carrier, leaving S.H.I.E.L.D. caught off-guard and Spider-Man left to single-handedly stop the assault. He assembles a new team, including an apprehensive Scarlet Spider, in order to stop the villains from taking over New York.