Norman Osborn, still with the Goblin in control tries to use the Transporting device to find out Spider-Man's secret identity. This leads to a fateful confrontation between Spider-Man and The Green Goblin that will change the wall-crawller's life forever.

The Green Goblin and the Hobgoblin clash over Dr. Ohn's Time Dilation Accelerator. Meanwhile Felicia is engaged to a smug playboy of whom Peter is greatly suspicious.

When Eddie refuses to continue to work for Dormammu, Carnage is considered sufficient to collect life-force which is essential for Dormammu to enter Earth. Carnage kidnaps Dr. Ashley Kafka, whom Eddie has fallen in love with. Eddie then reluctantly teams with Iron Man and Spider-Man to save her.

The symbiote returns to Earth and travels to Ravencroft to reunite with Eddie Brock, who then escapes as Venom. He is ordered by Dormammu, to whom the symbiote owes its earthly return, to steal a machine from Stark Enterprises capable of releasing Dormammu from his own far-off dimension.

Dr. Jonathon Ohnn was a brilliant scientist who created the Time Dilation Accelerator portal-making machine for Tony Stark, a.k.a. Iron Man. But after Iron Man and Spider-Man defeated Venom and Carnage, when they tried to free Dormammu from another dimension with the machine, he shut down the Accelerator. Ohnn quit and was later approached by the Kingpin who funded Ohnn's research to have him continue the Accelerator project and Ohnn fell in love with his partner, Dr. Silvia Lopez, who wanted to seek greater reward for her efforts. After they completed the machine, Ohnn was accidentally sucked into a portal, where numerous other portals were formed onto him, and he could create and recall the portals. Ohnn called himself the Spot and started stealing money to help fund his project go further.

Tombstone is hired by Alisha Silver to destroy the story planned for the Daily Bugle revealing that she had taken over her father's criminal organization, in exchange for large amounts of cash. Tombstone attempts to use Robbie Robertson, whom he was childhood friends with, to kill the story, using Robbie's teenage son Randy to do it.

Angry over his son's arrest and conviction, as well as Spider-Man now knowing his secret identity, to which he blames Alistair Smythe, Kingpin attempts to kill Spider-Man by turning Smythe into a cyborg to let him do it. Smythe's father is revealed to have survived the explosion in this episode, but the Kingpin has put him in cryogenic suspension.

Spider-Man has teamed with the Daredevil aka Matt Murdock, in an attempt to clear Peter Parker's name from crimes of treason, to which Daredevil informs him of Wilson Fisk's true identity as the Kingpin. As Spider-Man battles The Chameleon, the stage is set for a fateful showdown between Daredevil and The Kingpin.

Peter Parker is framed by Richard Fisk (son of Wilson Fisk, aka the Kingpin) for selling government secrets to foreign organizations. Peter meets with Matt Murdock, a blind but talented Defense Attorney who masquerades as the vigilante Daredevil.

Spider-Man finds himself in competition with himself over Felicia. Meanwhile, Jackson Weele leads a gang of thieves armed with jet-pack technology. Weele has developed a large gyro-wheel in which he uses to plunge through the city. Robert Farrell tries to help his ailing mother by using science and the gang's technology to arm himself as the "Rocket Racer".

While developing a new gas for the Kingpin to use as a weapon, a mistake triggers an explosion and Norman Osborn disappears in the chaos. A new villain, the Green Goblin appears and kidnaps all of Osborn's enemies.

During Spider-Man's battle with Octobot, he receives a head injury that gives him amnesia. Dr Octopus takes advance of this and convinces Spider-Man that he's his personal assistant and goes on a crime spree.

In a battle with Dr. Octopus a medical research building is destroyed. Blaming himself, Peter is considering giving up being Spider-Man, when he meets a mystic figure named Madame Web and his biggest fan, a little girl called Taina. Spider-Man shares his origin with her. Dr. Octopus attacks with his new invention the Octobot.

Mary Jane has joined a cult under the control of Baron Mordo, being led to believe that she has a relationship with her father. As Spider-Man investigates the truth behind the Cult's intentions, he has a meeting with Dr Strange and aids him in preventing Mordo from unleashing his dread master Dormammu from the dark dimension.