Episode 1 -Origins
After being bitten by a radioactive spider, Peter uses the five steps of scientific method to diagnose what has happened to him.
Episode 2 -Horizon High: Part 1
Peter Parker is accepted into Horizon High, a school for geniuses like Anya Corazon and Miles Morales. After Spider-Man stops a Vibranium machine that was secretly sabotaged by Spencer Smythe, his best friend Harry Osborn gets suspended by Max Modell pending an investigation when Spencer claims that Harry sabotaged the machine. Peter makes his debut as Spider-Man and must battle the Vulture when he targets his former employer Max.
Episode 3 -Horizon High: Part 2
After stopping the Scorpion from robbing the science museum, Peter works to obtain money to help Aunt May pay the bills. While meeting prodigy student/class advisor Otto Octavius, Max takes Peter in as a lab assistant. He is also told by Harry that his father Norman Osborn is creating the Osborn Academy for Geniuses as a way of saving him from the embarrassment after what happened at Midtown High. A giant robot secretly created by Spencer invades Horizon High, stealing some of Harry's devices just as Spider-Man creates a new costume.
Episode 4 -Osborn Academy
Following Spider-Man's fight with Jackal, Peter attends a tour of Osborn Academy alongside Max, Anya, Miles, and Gwen Stacy. Some of the students seen auditioning are Flash Thompson, John Jameson, Alistair Smythe, and Anya, in order to expand her background. Spider-Man faces two partners named Herman Schultz and Clayton Cole, who are divided over a spot as a student at Osborn during their audition and cause chaos with their sound manipulating machinery. However, Jackal has other plans as he steals their equipment while Harry continues to be suspicious of Spider-Man.
Episode 5 -A Day in the Life
As he juggles working with Max on the investigation on Harry Osborn, on a project for Otto Octavius' class, meeting with Harry, and a study group with Anya and Miles, Spider-Man catches Black Cat breaking into Horizon High to steal the V-252 symbiote from the space program, and tries to catch her despite being hit by her bad luck abilities. Meanwhile, Gwen's uncle Raymond Warren is rejected by Max for a position at Horizon High due to the accusations toward him at Empire State University.
Episode 6 -Party Animals
After Spider-Man stops another Slayer which self-destructs afterwards, Alistair gets frustrated as Norman welcomes him into Osborn Academy. With Harry cleared of the accusation upon the conclusion of the investigation, Max holds a dance on Saturday night as Norman tries to convince his son not to leave Osborn Academy. Meanwhile, Raymond attempts to join the Oscorp Academy where he pitches his hybridization project. After having been accidentally pricked by Raymond with a serum hidden at the bottom of his ring as part of his experiment, Aleksei Sytsevich mutates into Rhino.
Episode 7 -Sandman
While at Coney Island with his classmates, Spider-Man battles Sandman and retrieves a sample of him. When Sandman returns for the sample, he reveals he is trying to reach his daughter Keemia. Spider-Man discovers that Sandman's old boss Hammerhead was behind dumping a ton of sand and toxic waste on him. Both of them work to rescue Keemia from Hammerhead, only to find that the accident that Hammerhead caused also affected Keemia, turning her into Sandgirl. Meanwhile, Gwen, Anya, and Miles work on their analysis of the V-252 for the upcoming Stark Expo where it starts to get attracted to Peter.
Episode 8 -Symbiotic Relationship
Following the V-252 bonding to him following his fight with Keemia and Hammerhead, Spider-Man thwarts a robbery with A.I.M. only to discover the symbiote is not what it appears to be. He also learns that Norman has freed Vulture from prison and hired him as a professor at Osborn Academy while covering up the fact that they want to steal the V-252. Norman and Adrian Toomes allow Alistair to borrow the upgraded Vulture suit in order to infiltrate Horizon High.
Episode 9 -Stark Expo
After separating himself from the V-252, Spider-Man attends the Stark Expo and has an encounter with Iron Man who mistakes him for an intruder. Peter then tries to find Max in order to get him to not use the V-252, as he has trouble confirming his theory. At the same time, Osborn Academy is planning to introduce the Vulture Force made from Vulture's technology. The Stark Expo is then crashed by Ghost who steals the inter-connectivity disks to take control of everything at the Stark Expo. Spider-Man has to make a risk to use the V-252 to help fight Ghost and to prove to Max the truth about the V-252.
Episode 10 -Ultimate Spider-Man
While trying to get the spider from the experiment that granted Peter his powers, Spencer attacks Oscorp with a Spider-Slayer that he previously stole from Norman, only to bump into Miles outside of Oscorp. One such spider called the Electrolis Arachnatis escapes and bites Miles, giving him powers as well. Spencer is in allegiance with Raymond, who somehow got out of prison so that they can experiment with the eight spiders as part of their plot against their mutual enemy Norman. Peter has to stop Miles from going all out, which leads to both Spencer (on Raymond's behalf) and Alistair (on Norman's behalf) attacking Miles' neighborhood with giant Spider-Slayers.
Episode 11 -Kraven's Amazing Hunt
After Spider-Man trains Miles in battle with Scorpion, they find that he was being used by Kraven the Hunter so that he can hunt them on the latest episode of his TV show "Kraven's Amazing Hunt". They are unaware that Kraven has been hired by Norman to bring both Spider-Men to Oscorp for experimentation after the Spider-Slayer's failure to retrieve the stolen spider specimens. When Kraven starts veering from his deal with Norman, this causes him and Vulture to take matters into their own hands.
Episode 12 -Halloween Moon
On Halloween, Spider-Man, Harry, and Gwen assist the Hulk subdue a gamma-powered Man-Wolf before he infects the attendees of Horizon High's Halloween party and all of Manhattan enough to turn them into werewolves.
Episode 13 -Spider-Man on Ice
During a heat wave, Peter unknowingly helps the police to catch Hammerhead's minion Randy Macklin. As Harry shows off his cryogenic gauntlet to Peter, Macklin gives the police the slip. After claiming the diamond he placed in Peter's backpack and stealing the cryogenic gauntlet, Macklin adopts the alias Blizzard and begins his own crime spree, betraying Hammerhead. Spider-Man has to compete against Harry's thermal gauntlet when it comes to defeating Blizzard and reclaiming the cryogenic gauntlet.
Episode 14 -Venom
The V-252 mysteriously finds a new host, although it is currently locked up in Avengers Mansion. Spider-Man finds that the symbiote is not setting off his Spider-Senses. At the same time, Peter tutors Flash in his science exam overseen by his teacher Sal Salerno. Afterwards during the football game at Midtown High's rival Harry S. Truman High led by its quarterback Kevin Wyatt, Spider-Man finds that the V-252 had attached itself to Flash during the game. Spider-Man works to stop the symbiote's rampage even when the other football players get infected.
Episode 15 -Screwball Live
Following Spider-Man's fight with Absorbing Man, he encounters Screwball and disrupts her prank at the opening at a power plant that is polluting and working for an anonymous benefactor, albeit unaware that Screwball is actually Liz Allan. Hammerhead wanted Absorbing Man to steal the drive containing incriminating evidence on Hammerhead that is in Owl's possession, which was taken by Spider-Man during the fight. During Screwball's prank on Robbie Robertson by taking over a Worker-Bot made by Oscorp for helping at the New Media Building construction site, Absorbing Man begins to target Screwball in order to draw out Spider-Man by attacking Midtown High. Spider-Man must both rescue Screwball and Randy Robertson and defeat Absorbing Man and Hammerhead.
Episode 16 -The Rise of Doc Ock: Part 1
When Otto Octavius is caught in an explosion that fuses his robot arms to his body during his fight with Crimson Dynamo, Spider-Man sees the opportunity to recruit the "Octopus" into becoming a hero when it comes to tracking down Dynamo.
Episode 17 -The Rise of Doc Ock: Part 2
Spider-Man invites Octavius to patrol the streets alongside himself and Miles until it becomes clear that Otto is not exactly a team player, though they will have to work together when Oscorp scientist Dr. Curt Connors becomes Lizard.
Episode 18 -The Rise of Doc Ock: Part 3
Peter spends a day at Osborn Academy in the hopes of finding a clue that will convince Harry that his father is out to destroy Spider-Man. During this time, Peter meets the latest student Oliver Osnick. While Octavius is annoyed that Norman has started developing the Octobots without his approval, Aleksei is once again duped by Jackal into turning the Osborn Academy students into Rhinos like him.
Episode 19 -The Rise of Doc Ock: Part 4
After he and Miles find that the Raymond at New York Penitentiary is an explosive clone, Peter must team up with Gwen and a reluctant Harry to investigate the truth behind the missing Raymond. When they come across the underground lab upon finding the entrance at Midtown High, it is discovered that the remaining genetically-altered spiders are being used to make an army of Jackal clones with spider powers. They are unexpectedly joined by Norman and the Osborn Commandos (consisting of Octavius, Alistair in one of his Spider-Slayers, Vulture, Rhino, and Oliver). But when the real Jackal shows up, Octavius betrays the group and turns his teammates into the Sinister Five.
Episode 20 -Spider-Island: Part 1
Spider-Man and Miles track down an unidentified villain with Spider Powers who steals Peter's experimental stealth suit and equipment from both Horizon High and Oscorp Academy. To their surprise, Gwen has developed spider powers and has become Spider-Gwen after being exposed to the chemicals from Jackal's altered spiders. With unlikely help from Harry (whom Gwen has convinced to no longer blame Spider-Man for Norman's apparent death), Spider-Man, Miles, and Spider-Gwen must stop the unidentified villain from setting off a weapon at the Statue of Liberty.
Episode 21 -Spider-Island: Part 2
When everyone in Manhattan starts manifesting spider powers, Spider-Gwen follows Spider-Man into thwarting a robbery by Hydra operative Crossbones. While Anya starts developing spider powers and gets a hold of them, Spider-Man and Spider-Gwen must help Black Widow track down Crossbones and his Hydra team when they plan to rob the Vibranium storage vault on behalf of Arnim Zola.
Episode 22 -Spider-Island: Part 3
Peter must find a way to cure Gwen after finding out she had mutated into a Man-Spider. Things get harder when Kraven the Hunter resurfaces and turns New York into his hunting grounds as part of his latest episode. Spider-Man, Harry, Kraven, and Anya discover that the Man-Spider who stole Peter's stealth suit was a mutated Norman.
Episode 23 -Spider-Island: Part 4
When more people turn into Man-Spiders, Peter and Harry must battle through an island of Man-Spiders to get to Norman, who appears to be controlling them all as the "Spider King". When their attempted cure only restores Norman's mind and not his body, Peter infuses the antidote with his own blood. The boys also discover the real mastermind behind the Man-Spider crisis is none other than the Jackal.
Episode 24 -Spider-Island: Part 5
After being captured, Spider-Man discovers that Jackal had previously captured Miles, which explained why he could not be reached. Jackal considers both Peter and Miles to be the first Spider Soldiers. In order to cure the Man-Spider population of Manhattan, Spider-Man must lead Miles, Anya, and Harry on a desperate last-ditch effort to stop the Jackal.
Episode 25 -The Hobgoblin: Part 1
Following the Man-Spider crisis and the destruction of Osborn Academy, Norman graduates Harry and gives him the Hobgoblin armor and equipment. Meanwhile, Spider-Man takes on Dr. Octopus and his Sinister Five before they can brainwash him, thereby renaming the group the Sinister Six, and destroy New York City.
Episode 26 -The Hobgoblin: Part 2
After having rounded up the rest of the Sinister Five, Spider-Man and Hobgoblin work to find Doctor Octopus. However, after capturing Doctor Octopus when he attacks Horizon High, Spider-Man is suddenly attacked by Hobgoblin. Spider-Man must find a way to stop Hobgoblin who is completely bent on destroying Spider-Man by any means necessary. However, Spider-Man discovers that "Hobgoblin" is actually someone he least suspects and Harry must choose between siding with either his best friend or his father.