With most of his fellow students replaced with synthezoids, Spider-Man must work with Agent Venom and Rhino to rescue their classmates and defeat Arnim Zola.

The security system at Aunt May's home becomes dangerous.

Peter Parker scrambles to focus his attention between completing his science fair project with Luke Cage and combatting Juggernaut. In his desperation concerning the first case, he decides to "borrow" one of Dr. Connor's inventions ... which (literally) becomes an even bigger threat to the city.

When Rhino learns that his archenemy Flash has become a hero, he starts a bitter rampage through New York. Spider-Man and Agent Venom are the last line of defense with help from Hulk. However, Hulk and Rhino face in battle and only Spider-Man and Agent Venom should stop now so to not cause destruction.

When Spider-Man and his fellow teenage super heroes cause too much damage in a super villain fight, Nick Fury assigns them to work with the super clean-up company Damage Control. While working with Damage Control, Spider-Man uncovers a villainous mystery.

Loki exacts revenge on Spider-Man by turning him into a pig, just in time for the Asgardian Boar Hunt across New York City. Now, Thor, who knows all too well how it feels to be transformed into a helpless animal, must help Spider-Ham survive.

A disgruntled Stark Industries scientist named Michael Tan develops and envelops himself in a swarm of self-replicating nanobots. Now Spider-Man must work with Iron Man to contain Swarm.

Nick Fury has been infected by nanite versions of Doctor Octopus' Octo-Bots. While the others face off against Doctor Octopus, Spider-Man and Power Man work with Ant-Man to enter Nick Fury's body and get the Octo-Bots out of him.

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.

Flash Thompson stars as Spider-Man in a Midtown High musical production, and gets a taste of what Spider-Man's life is really like when the Trapster mistakes the football jock for the real web-slinger.

Spider-Man travels to the moon to rescue J. Jonah Jameson's son, but a bizarre threat awaits him on the lunar surface.

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.

Trick-or-treaters start turning into monsters and Spider-Man, Dr. Strange and Ant-Man must team up to stop Baron Mordo.

Spider-Man accepts an invitation from Boston to become the city's official hero.

Spider-Man, Iron Spider, Agent Venom, Kid Arachnid, and Scarlet Spider have been looking for signs on where Doctor Octopus is hiding out. Upon Spider-Man and Iron Spider being ambushed by Vulture, they follow him to a nearby island where they are attacked by clones of Sandman. As Spider-Man fights the Sandman clones, Iron Spider stumbles upon a secret laboratory where Doctor Octopus has captured Sandman and cloned him so that he can find the "Ultimate Sandman" that will join the Sinister Six. After Sandman is rescued and Doctor Octopus escapes, Spider-Man allows Sandman to spread out around the Triskelion.

During a drought, Spider-Man, Iron Spider, Kid Arachnid, and Scarlet Spider answer a distress signal that takes them to an abandoned mall in Queens. They find an empty air-tight room containing Hydro-Man who has a past with Nick Fury. While transporting him to the Triskelion, Iron Spider find that Hydro-Man is not a good guy where the fight with him causes an emergency landing near Aunt May's house. While Spider-Man, Iron Spider, and Kid Arachnid fight Hydro-Man, Scarlet Spider works to protect Aunt May who ends up naming him Ben. Once Hydro-Man is defeated where the resulting battle watered Aunt May's lawn, Spider-Man gets word that the Quinjet carrying Hydro-Man back to his cell was intercepted causing Spider-Man to speculate that Doctor Octopus has gotten Hydro-Man on his side.

When a battered Nova asks for help finding Nick Fury, Spider-Man tracks him to the dangerous ruins of an ancient city.

Spider-Man and Miles, tracking the missing pieces of the Siege Perilous, travel to a tropical Pirate dimension where they meet Web Beard, the Spider-Pirate, and encourage him and his old team to work together to save themselves from the dreaded Kraken.

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.

Aunt May goes on a date with Phil Coulson, Peter's principal and S.H.I.E.L.D. supervisor, and the Beetle returns to continue his evil deeds.

Spider-Man and Hawkeye join forces when the Beetle returns to New York City.

After Spider-Man finally ends up back 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 to battle the Spider-Goblin and save New York even when Electro plans to destroy it.

The S.H.I.E.L.D. Academy has been opened up at the Triskelion by Nick Fury as Spider-Man's group gets their education from Mr. Frank and guest instructors like Captain America and Hawkeye. Halfway into their education, Spider-Man and Iron Spider unknowingly reactivate an old World War II villain named Arnim Zola.

Following Spider-Man's fight with Molten Man, the Inhumans have declared war on Manhattan as Nick Fury blames the exchange student Triton. Spider-Man and Triton discover that Maximus has brainwashed the rest of the Inhuman Royal Family (consisting of Black Bolt, Medusa, Gorgon, Lockjaw and Karnak) and plans to crash Attilan into Manhattan.

After Doctor Octopus and Rhino have escaped the Triskelion with Agent Venom in their clutches, Spider-Man and Scarlet Spider track them to the recently-returned HYDRA Island as Doctor Octopus and Arnim Zola work to separate the Venom symbiote from Flash Thompson. In order to get to Flash, Spider-Man and Scarlet Spider have to fight their way past Kraven the Hunter and the HYDRA Agents. Ock Manages to succeed in separating the symbiote from Flash, giving to Kraven, who becomes a lion-like Venom. However, Flash is able to coerce the symbiote back to him as they understand each other. As a result of the re-fusion, Agent Venom gains a new look.