During the boss fight against Wolverine, he is convinced that Spider-Man is stuck in the Black Symbiote Suit. To prove his authenticity, Wolverine asks Spider-Man various multiple-choice questions about his life and their history together:

• "What are your parents names?" - Spoiler:Richard and Mary Parker. This serves as a reference to the 1995 comic Untold Tales of Spider-Man, where it's shown that Wolverine met Peter Parker's parents during their time as spies.
• "Whose killers did we track in Berlin?" - Spoiler:Ned Leeds. This calls back to the 1987 Spider-Man Vs. Wolverine one-shot, in which the aforementioned character is killed while on assignment for The Daily Bugle in Berlin.
• "Where did you first wear the Black Suit?" - Spoiler:Battleworld. This is a reference to Secret Wars issue #8, where the Black Suit originates from.
• "Who declined joining the New Avengers?" - Spoiler:Daredevil. During issue #3 of the New Avengers comic series in 2005, Captain America offers this character a position in the team, to which he declines.
• "What is Critical Mass?" - Spoiler:A Mutant. This is a reference to Marvel Comic Presents #49 featuring the rotund Critical Mass, who Spider-Man in-game describes as "That Blob wannabe with electric fingertips."
• "Who served us Roast and Pie?" - Spoiler:Aunt May. Calling back to issue #4 of Spider-Man & Wolverine in 2003, in which the aforementioned character feeds Wolverine a similar meal.