Peter Parker learns Doctor Octopus has teamed up with Arnim Zola and Hydra to attack the Tri-Carrier, leaving S.H.I.E.L.D. caught off-guard and Spider-Man left to single-handedly stop the assault. He assembles a new team, including an apprehensive Scarlet Spider, in order to stop the villains from taking over New York.

After being saved by Scarlet Spider following Arnim Zola's takeover of the S.H.I.E.L.D. Tri-Carrier, Spider-Man must work with him to liberate Manhattan and his fellow students from HYDRA's clutches. Even when they save Agent Venom and Iron Spider, they must also undo transformations of the HYDRA Goblins, avoid Doctor Octopus and Kraven the Hunter, and defeat Arnim Zola.

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.

With the Siege Perilous destroyed in the aftermath of the fight with the Ultimate Green Goblin, Miles Morales is forced to stay in Spider-Man's reality until S.H.I.E.L.D. can find a way to get him and his world's Goblin back to their home. Now dubbed Kid Arachnid, he and Spider-Man must help Norman Osborn when he is targeted by Doctor Octopus and Vulture.

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.

After Doctor Octopus and Rhino have escaped the Triskelion with Agent Venom in their clutches, Spider-Man and Scarlet Spider track them to the recently-returned HYDRA Island as Doctor Octopus and Arnim Zola work to separate the Venom symbiote from Flash Thompson. In order to get to Flash, Spider-Man and Scarlet Spider have to fight their way past Kraven the Hunter and the HYDRA Agents. Ock Manages to succeed in separating the symbiote from Flash, giving to Kraven, who becomes a lion-like Venom. However, Flash is able to coerce the symbiote back to him as they understand each other. As a result of the re-fusion, Agent Venom gains a new look.

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

Spider-Man and Kid Arachnid travel to alternate dimensions to gather the shards from the broken Siege Perilous.

Spider-Man and Miles, tracking the missing pieces of the Siege Perilous, travel to a tropical Pirate dimension where they meet Web Beard, the Spider-Pirate, and encourage him and his old team to work together to save themselves from the dreaded Kraken.

Returning to the Noir reality, Spider-Man and Kid Arachnid tangle with Mr. Fixit (a Noir version of the Hulk) and his minions Thunderbolt and A-Bombardier, who are in a gang war with the Noir version of Hammerhead. When Spider-Man Noir shows up, he doesn't want Spider-Man and Kid Arachnid to break up the gang war because since they last saw him, he lost his Mary Jane in an accident caused by Hammerhead's gang, for which he blames Mr. Fixit. Spider-Man finds the Siege Perilous fragment in the new machine gun that was provided by Hammerhead's minion Martin Li. Upon touching the Siege Perilous, Martin Li becomes the Noir version of Mister Negative in order to become the new crime lord; he can transmutate anything to stone, and overthrows Noir Hammerhead. After Noir Mister Negative fends off Wolf Spider, Spider-Man and Kid Arachnid must persuade Spider-Man Noir and Noir Mr. Fixit to work together to help defeat Mister Negative.

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

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.

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.