Season 01 Episode 11 -The Hobgoblin, Part 1
Norman Osborn hires the Hobgoblin to assassinate Wilson Fisk, also known as the Kingpin, because of the crime lord's continuous threats against him. Peter Parker saves Fisk just as the Hobgoblin attempts an attack on him. After eluding Spider-Man, the Hobgoblin is fired by Norman as of his unsuccessful assassination on the Kingpin.
Season 02 Episode 07 -Chapter VII: Enter the Punisher
An increasingly desperate Spider-Man drinks the serum designed to cure him, but it makes him grow four extra arms. Marvel anti-hero Punisher thinks Spider-Man is a crook and chases him around. Spider-Man finds out that Michael Morbius has turned into a vampire and is draining people's blood to survive. Spider-Man wants to help Michael, but the Punisher is trying to get rid of Spider-Man at the same time.
Season 02 Episode 11 -Chapter XI: Tablet of Time
An ancient artifact known as the Tablet of Time has been uncovered. Kingpin wants to sell it, while elderly Silvermane wants to use it to restore his youth. Each crime lord kidnaps a useful hostage and a useless hostage.
Season 02 Episode 14 -Chapter XIV: The Final Nightmare
Spider-Man seeks Curt Connors' aid to help reverse the aging effects of the Vulture's talons. After absorbing Spider-Man's youth, and DNA, the Vulture mutates into the Man-Spider. Meanwhile, the Scorpion grabs Dr. Farley Stillwell to seek a cure for his own mutation.
Season 03 Episode 01 -Chapter I: Doctor Strange
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.
Season 03 Episode 02 -Chapter II: Make a Wish
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 an inter-dimensional being 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.
Season 03 Episode 03 -Chapter III: Attack of the Octobot
During Spider-Man's battle with Octobot, he uses a nerve nullifying blaster to give him amnesia. Dr. Octopus takes advantage of this and convinces Spider-Man that he's his personal assistant and goes on a crime spree. Taina manages to get Spidey to remember his true self; he then returns her back to her room, where he even reveals his true identity to her. Taina promises never to tell anyone. Spidey thinks to himself that Taina was a bigger hero than himself. The last scene of the episode shows Taina is in a facility for terminally ill children, and meeting Spidey was her last wish.
Season 03 Episode 04 -Chapter IV: Enter the Green Goblin
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.
Season 03 Episode 05 -Chapter V: Rocket Racer
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".
Season 03 Episode 06 -Chapter VI: Framed
Peter Parker is framed by Richard Fisk (the 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.
Season 05 Episode 09 -Chapter I: Arrival
Madame Web brings Spider-Man to another dimension where he is brought before a being known as the Beyonder, who has chosen Spider-Man to be part of an experiment to see if good is more powerful than evil. He finds a paradise planet and introduces a band of villains to take it over (Doctor Octopus, Doctor Doom, Alistair Smythe, The Lizard, and the Red Skull), and it's up to Spider-Man to lead a team of superheroes to save the planet. Spider-Man summons The Fantastic Four, Iron Man, Captain America, and Storm from the X-Men. Before he can explain, The Thing and The Human Torch attack him, but the others defend him. The Lizard then appears and attacks Spider-Man, but they knock him unconscious. They manage to agree to a team up and use the alien tech to reactivate the part of the Lizard's mind in which Dr. Conner's consciousness is; now in control of himself, Conners sides with Spidey's team.
Season 05 Episode 10 -Chapter II: The Gauntlet of the Red Skull
Dr. Octopus and Alistair Smythe join forces with the Red Skull. Spider-Man brings Black Cat to the planet to help him, although at a bad time as she, Morbius and Blade were battling Mirium and her vampires. Along with Captain America, Iron-Man, and The Lizard (who has switched sides), they cross a wasteland in order to launch an assault on the Red Skull's empire.
Season 05 Episode 11 -Chapter III: Doom
After defeating the Red Skull, Spider-Man and the team attempt to rendezvous with the Fantastic Four, only to discover that they have been ambushed and that Dr. Doom has kidnapped The Thing. The heroes all go to rescue him, entering Dr. Doom's empire, which they discover is a peaceful paradise. Doom used the technology of the planet to not only dethrone Doc Ock, but make his New Latverria a place of good; he even gave Thing a watch to switch him back to his normal self. After learning of the Beyonder's powers, Doom decides to absorb him to ensure eternal peace by banishing the other villains; however, demons pop out of his dreams. Spidey is able to reverse the process, proving Good is superior. Beyonder erases the others' memories and sends them back to where and when they were taken. He then reveals to Spidey that this was a test to show if he was worthy of the true challenge.
Season 05 Episode 12 -Chapter I: I Really, Really Hate Clones
Spider-Man is taken to an alternate dimension where due to a series of events, its native Peter Parker has bonded with the Carnage symbiote to become the maniacal Spider-Carnage, who has devastated and demolished New York City with the aid of the Kingpin, Alistair Smythe, the Hobgoblin and the Green Goblin. The Beyonder tells Spider-Man that his deranged counterpart plans to use a matter-disintegrator bomb powered by the Time-Dilation Accelerator to destroy the entire multiverse, and the only way to stop him is for Spidey to lead a group of Spider-Men from different dimensions to prevent the blast. Unfortunately, one of the Spider-Men is suffering from the six-armed mutation; he turns into the feral Man-Spider mid-mission.
Season 05 Episode 13 -Chapter II: Farewell, Spider-Man
The Spider-Men stop Spider-Carnage in his home dimension, but he escapes to another dimension, the one where Spider-Man is a billionaire. With limited power Madame Web sends the original Spider-Man to this dimension, where he finds himself engaged to Gwen Stacy, and finds Mary Jane alive. Though it seems Spider-Carnage can't be stopped, this reality is where Peter Parker made the right decisions; a still-alive Uncle Ben manages to bring the real Peter's personality out of Spider-Carnage, but the symbiote is too strong. Spider-Carnage jumps into an unstable portal that destroys him. When all the Spider-Men are being returned home, the powerless one explains that in his world, he's an actor that portrays Spider-Man and that he is a fictional character. Spidey journeys to that world, where he meets his creator, Stan Lee, and takes him web-swinging as thanks for creating him. Madame Web then takes Spider-Man to find Mary Jane as a reward for saving reality.