Dr. Curt Connors has been turned into Lizard again. This time, he has a bite that turns anyone who is bitten into Lizards. The Triskelion goes under lockdown when Spider-Man's team and the S.H.I.E.L.D. Academy personnel get infected and attack Spider-Man. With help from an item in Nick Fury's office and with the help of Iron Spider, Leo Fitz, and Jemma Simmons, Spider-Man must work on an antidote in order to restore everyone to normal. Meanwhile, Agent Venom and Rhino guard Doctor Octopus' cell during the outbreak just in case he plans any escapes from his cell. Once everyone is cured, Spider-Man witnesses Doctor Octopus and Rhino making off with Agent Venom.

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.

Spider-Man and Agent Venom have been busting villains like Beetle, Grizzly, Shocker, and Shriek where they suspect that they might be candidates for Doctor Octopus' Sinister Six. Arnim Zola recruits Michael Morbius to work on a new symbiote. When Spider-Man, Agent Venom, and Harry Osborn in the Patrioteer armor track them down, they are caught off-guard when they release the Anti-Venom symbiote which possesses Harry and does not have any of the symbiote weaknesses. The resulting battle leaves Agent Venom injured and Harry in a coma.

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.

Spider-Man faces the culmination of all Doc Ock's evil machinations when the new Sinister Six assaults the Web Warriors and S.H.I.E.L.D. Academy at the Triskelion.

When Doc Ock learns that the key to a device that will retrieve Hydra Island is at Aunt May's house, Spider-Man must fight to protect his family.

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

Spider-Man, having collected all of the shards of the Siege Perilous, returns to Miles Morales' universe and confronts Wolf Spider.

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

Spider-Man must team with the former traitor, Scarlet Spider, to stop Doc Ock from reawakening a secret program designed to create evil duplicates of Spider-Man.

Spider-Man and Scarlet Spider have to infiltrate the sunken Hydra Island so Scarlet can destroy the lab that created him.

Spider-Man puts the Triskelion on lockdown when a mysterious villain begins to take out the heroes one at a time.

Spider-Man house sits on Christmas Eve and is forced to team up with Moon Knight to defend the home from the new Mysterio.

Spidey must track down Ock before he harms Aunt May.

Peter Parker must find a way to stop Doctor Octopus and the Superior Sinister Six from destroying all of the heroes in New York and taking over the world.

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.

After learning that Norman Osborn injected himself with an Anti-Goblin serum to prevent further transformations into Green Goblin following the last encounter, Doctor Octopus teams up with Baron Mordo and uses the Siege Perilous to pull the Ultimate Green Goblin from Miles Morales' universe into theirs so that HYDRA can be his master. Now Spider-Man and Miles have to work together with Doctor Strange to keep the demonic Goblin from using the Siege Perilous to destroy reality.

Under the supervision of Osborn, Doctor Octavius obtains a sample of Spider-Man's blood in order to create a creature that rivals the powers of the wall crawler. Meanwhile, Peter attempts to balance his friendship with Harry with his time with his SHIELD teammates.

While on a field trip, Spider-Man and his superhero friends encounter the mighty Thor, who is transformed into a frog by his mischievous half-brother Loki. Now, the heroes must venture to the magical world of Asgard in order to save the nine realms from Loki's wrath.

When New York is plunged into a mystical sleep, Iron Fist and Spider-Man (who is at first highly sceptical of magic) seek the help of Doctor Strange. In order to break the spell, the three heroes must face their own worst fears in the face of the spell's initiator, the extradimensional entity known as Nightmare.

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.

After being late for training, Spider-Man is faced against an evil super army called Zodiac and their leader, Scorpio, who took over the S.H.I.E.L.D. Helicarrier and set it on self-destruct. Spider-Man and Fury must put their differences aside and fight the new menace as a team.

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.

When Phil Coulson wants the heroes to report to the S.H.I.E.L.D. ice base for winter survival training, Spider-Man and his team sneak off for a vacation on a deserted tropical island that Nova finds under "classy." However, they soon realize something is not right with the island and the Sandman will make sure they never leave.