When Mister Sinister returns to his laboratory he spends the next several hours studying Spider-Man only to learn that he is not a true mutant. This makes Mister Sinister angry because he feels as if he wasted his time. Mister Sinister then tries to convince Adam that Spider-Man is evil and attempts to get him to harm Spidey with his pyrokinetic powers.
At that moment Gambit returns to Empire State University and sees that the science building is on fire. Gambit rushes inside the building and is able to get Beast and Curt Connors to safety. Beast tells Dr. Connors that Mister Sinister is one of the X-Men's greatest enemies. Dr. Connors then gives Beast one of Spider-Man's Spider-Tracers that he dropped before Sinister took him. Beast informs Dr. Connors that if he can reverse the Spider-Tracer's signal they can use it to locate the receiver and find Spider-Man.
Back at Mister Sinister's laboratory, Spider-Man tries to tell Adam that Sinister is not his friend while Mister Sinister tries to convince Adam that Spider-Man is his enemy and to use his powers to harm him. However, before Adam can do anything Beast and Gambit barge into the laboratory. Mister Sinister then calls in the Nasty Boys and they attack the X-Men. While Mister Sinister is busy watching the Nasty Boys fight the X-Men, Spider-Man is able to break free from his shackles and joins the fight.
With the Nasty Boys failure to defeat Beast, Gambit, and Spider-Man, Mister Sinister orders them to stand aside so he can take care of the heroes himself. However, after a brief fight Sinister’s machines finish collecting Adam’s DNA. Mister Sinister reveals that he plans to use Adam’s DNA to create an army of unstoppable super mutants. Mister Sinister and then escape.
Right after Mister Sinister and the Nasty Boys get away, Adam begins to lose control of his power. Spider-Man goes up to Adam and tells him that because he is different it has allowed him to help people and go places that he wouldn't be able to if he were normal. Spider-Man starts to pull off his mask to reveal his identity to Adam. However, Adam calms down and stops Spider-Man from revealing his identity. Adam realizes that Spider-Man understands how he feels. Adam then tells Spider-Man and the X-Men that he wants to go back to the orphanage to teach the other kids that being different isn't a bad thing.
- Mister Fantastic / Reed Richards (Mentioned only)
- The Avengers (Mentioned only)
- Doctor Doom / Victor Von Doom (Mentioned only)
- Venom / Eddie Brock (Mentioned only)
- When Gambit enters Mister Sinister's laboratory, he mentions Paul Prudhomme who was a real celebrity chef that specialized in Creole and Cajun cuisine.
- Beast mentions that the last time the X-Men fought the Nasty Boys was in a jungle in the South Pacific Ocean. This is a reference to the episodes Reunion, Part I and Reunion, Part II from X-Men: The Animated Series.
- When Adam starts to lose control of his power, Spider-Man states that he is "he's burnin' like a super nova." A super nova is a star that suddenly increases greatly in brightness because of a catastrophic explosion that ejects most of its mass.
- Also, when Adam starts to lose control of his powers, Beast says "oh, my stars and garters" which is his catch-phrase in the comics.
- Spider-Man mentions Mount Vesuvius which is a volcano located in Campania, Italy. Mount Vesuvius is known for being the volcano that destroyed the Roman city of Pompeii.
- Spider-Man tells Adam that he helped the Fantastic Four and the Avengers fight an intergalactic war. This is possibly a reference to the 1984 limited series, Marvel Super Heroes Secret Wars. Secret Wars was later adapted into a three part episode    during the fifth season of Spider-Man: The Animated Series.