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Spider-Man and Scarlet Spider must overcome Kraven in order to rescue their kidnapped teammate, Agent Venom.
After Spider-Man and the Web Warriors are told by Vulture that there is a spy among the other heroes, he and the Web Warriors work to find out who it is while Nova and Nick Fury are away on a secret mission. They test out the new training area that was designed by Leo Fitz and Jemma Simmons, only to discover that the robots were sabotaged. Dr. Connors once again becomes Lizard and now sports a contagious bite that turns others into lizards. When everyone ends up infected, it's up to Spider-Man to stop the Lizard and cure everyone before the infection spreads out of the Triskelion. In the end, Rhino is revealed to be the spy as he and Doctor Octopus escape with Agent Venom as their prisoner.
Spider-Man and Iron Spider discover Doc Ock has taken control of Sandman.
As Season 4 begins, Doctor Octopus allies himself with Arnim Zola and HYDRA and begins to form a new iteration of the Sinister Six starting with Kraven the Hunter. When Doctor Octopus attempts to turn Norman Osborn back into Green Goblin, he finds that Osborn injected himself with an anti-Goblin serum to prevent further transformations. Doctor Octopus uses the Siege Perilous to summon the Green Goblin's demonic winged counterpart from Miles Morales's universe and after a brief battle recruits him instead. Then it is revealed that Rhino has become a spy for Doctor Octopus while operating as a student at the S.H.I.E.L.D. Academy in exchange for finding a cure for his condition (since he gained his powers by drinking one of Doc Ock's animal serums). Now titled Ultimate Spider-Man vs the Sinister 6, the show will see Spider-Man fighting evil with the help of S.H.I.E.L.D. and his own team consisting of Agent Venom, Iron Spider, Miles Morales (going by the name Kid Arachnid), and the newly introduced Kaine/Scarlet Spider, as well as S.H.I.E.L.D. operatives Leo Fitz and Jemma Simmons.