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 a childish argument between Spider-Man and Nova gets their entire team grounded, the super-youths go through S.H.I.E.L.D.'s database of the most wanted supervillains to see who they can defeat and apprehend in order to impress Nick Fury. When the choices Batroc the Leaper, Blizzard, Melter, MODOK, Toad, Whirlwind, and Lady Porcupine prove unpopular, Spider-Man and his team go to Latveria to track down Doctor Doom. The young heroes fairly easily capture Doom, but things take a turn for the worst when Doctor Doom tricks the team into taking one of his Doombots aboard the Helicarrier.
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's dream of joining the Avengers becomes a nightmare when Loki switches bodies with the web-slinger, turning his new teammates against him. / Spider-Man and his friends team up with the Avengers to stop Loki and Doctor Octopus from destroying New York City with an army of Venomized monsters.
Spider-Man realizes he has inspired a whole new generation of aspiring super-heroes and wants to encourage them to have S.H.I.E.L.D. training and form a new team, the New Warriors. However, Taskmaster and his Thunderbolts stage a surprise attack on the S.H.I.E.L.D. Carrier, and the New Warriors must face their first trial by fire when they strive to prevent a breakout of the Green Goblin, Dr. Octopus, Beetle and Scorpion.
Spider-Man finally ends up in his own universe, he finds Green Goblin has injected himself with the Spider-Men DNA from all the universes to become the Spider-Goblin. With Electro's help from the Siege Perilous he summons all the Spider-Men dubbed Web-Warriors and defeats the Spider-Goblin, but Electro turns on them and uses the Helicarrier to self-destruct and take out New York but is stopped with the help of Spider-Ham and Spider-Girl.
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.
Spider-Man and Agent Venom have been cracking down at defeating possible Sinister Six recruits like Shocker, Grizzly, and Beetle. When Doctor Octopus has made an entirely new symbiote even when Arnim Zola pairs him up with Dr. Michael Morbius, it takes control of Harry Osborn and now forces him to destroy Spider-Man and Agent Venom as the new Anti-Venom. Now Spider-Man and Agent Venom must work with Iron Patriot to free Harry from the Anti-Venom symbiote.