Judging from the synopsis for part two of the finale, it seems Spidey takes the option to nullify his powers and has to deal with the Sinister Six as just regular old Peter Parker
Part One's synopsis specifically mentions his Spider-Man guise
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Doctor Octopus (Doc Ock) threatens to harm Aunt May if Spidey ever puts on his mask again. Spider-Man must track down Doc Ock before he has a chance to put his plan into action.
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While part two has this:
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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.
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http://uk.ign.com/articles/2017/01/0...nimated-series