Michael Reaves and Will Meugniot came up with the show's story and the Counter-Earth setting to accommodate Marvel's needs.

Elements included on Marvel's 'shopping list' included Counter-Earth, the Knights of Wundagore, John Jameson, Deathlok, Venom, and others. Marvel gave the producers a list of what they wanted in the series. Sony's series became Spider-Man: The New Animated Series. The producers toyed with Spider-Man 2099 for about a week but realized that Batman Beyond had more or less appropriated that property's territory. Jonah Jameson briefly appeared in the first episode. This series would be able to use Spider-Man but none of his supporting characters or stories. As such, the show was unable to use the early comics or even the classic costume. However, Marvel and Sony Pictures Entertainment made a deal for a live-action film, which included their own series to use the same source as the film. This would have provided the additional season as cheaply as possible. The idea was to have Saban Entertainment simply crudely animate thirteen of the first twenty-six classic comics, known today as motion comics. The initial goal was to make an extremely low budget adaptation of the early issues of The Amazing Spider-Man and the show began production with that in mind. If Fox produced another season of a Spider-Man show, they could continue airing episodes for an undisclosed amount of time. Producer Will Meugniot explained that Spider-Man Unlimited was created because both Marvel Entertainment and Fox Kids needed another Spider-Man series to fulfill contractual obligations. It is soon discovered that Venom and Carnage are on Counter-Earth and are following orders from the Synobtic, a hive mind legion of Counter-Earth symbiotes. Spider-Man then agrees to stay on Counter-Earth, blending in as best he can as Peter Parker and fighting with the rebellion as Spider-Man. However, Jameson is reluctant to return until all the Beastials are defeated. Spider-Man attempts to get Jameson to return to Earth. However, Spider-Man learns that Jameson has joined the Counter-Earth's rebellion who is fighting against Counter-Earth's dictator, the High Evolutionary. Spider-Man then hijacks a space shuttle and flies to Counter-Earth to return Jameson to Earth. When Spider-Man fails to stop Venom and Carnage from stowing away on John Jameson's space shuttle to Counter-Earth he is blamed and creates a new spider suit made of nano technology borrowed from Mister Fantastic's laboratory.

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