Kraven the Hunter is in New York City to show off his prehistoric animals. However, his sideshow is a cover for his plot to take over New York City by hatching a dinosaur army. He steals a rare ruby (the Eye of India) and kidnaps Firestar to coerce her into harnessing her energy to power a growth energizer, which will hatch the eggs containing the dinosaurs.
Mr. Frump, a downtrodden, homeless man, gets ahold of an ancient amulet that Dr. Doom had hoped to use to gain control of the world. As Frump is realizing the amulet's powers (and making many new friends as a result), Dr. Doom plots to trick Frump into handing over the amulet.
The gang meets Sunfire, a mutant who has powers identical to those of Firestar. Sunfire reveals that his uncle Genju needs assistance in starting a fusion reactor which will supply power to the world, unaware that Genju simply wants to gain enough power so that he cannot be defeated in his quest to rule the world.
A meteor crashes into a beehive, creating a mutant creature that calls itself Swarm, whose body is made up of thousands of bees. Swarm - whose lair is a giant beehive, where the meteor radiating its power is housed - immediately begins mutating worker bees into huge drones, then begins zapping the residents of New York City into drones.
Electro plots to take over New York City by harvesting all of the city's electric power. To help him accomplish his scheme, he breaks into an arcade video game to create Videoman, an electronic being whose primary aim is to gather the needed supplies to create the giant transformer that will give Electro the unlimited power he desires ... and stop any Spider-Friends that get in his way.
The evil Magneto places a force field around a prison island, holding the prison staff and others attending a convention (including the Spider-Friends) hostage. Magneto seizes control of the power supply to the entire East Coast and threatens to destroy the Earth unless his "Brotherhood Of Evil Mutants" are immediately paroled from jail.
Spider-Man investigates a series of efforts to sabotage movie producer Sam Blockbuster's attempts to make a movie based on the web-slinger's life. Mysterio, who is revealed as the culprit, cons Blockbuster into having Spidey star as himself, as part of a plan to kill off his nemesis.
The Spider-Friends team with Thor to stop Thor's evil half-brother, Loki, in his effort to acquire the ancient Twins of the Gods gems. The gems will grant unlimited power to whomever holds both of them, and if Loki were to get them both, he would be unstoppable in wreaking havoc over New York City.
The Kingpin plots to steal the Omni-Blaster, a secret military weapon that would make him unstoppable as he goes on a daring crime spree. To ensure his success, he uses a special mind-control disc to turn Captain America and Iceman into his co-conspirators.
The Spider-Friends and Professor Hiawatha Smith follow the Red Skull to an African island, where he plans to use experimental Nazi weapons to start World War III. The Red Skull finds out that he's being tracked, has the Spider-Friends and Smith captured and straps them to the missiles.