A plot could involve Female Carnage being mind - controlled by an evil scientist. Spider - Man has to break the control without harming her. In the process, they form an unexpected alliance. They might also discover that the scientist has ties to both of their pasts, which adds an interesting layer to the story.
One idea could be that Female Carnage has some information about a new super - villain who is planning to destroy the city. Spider - Man has to work with her to get that information, even though he doesn't trust her. Along the way, they start to understand each other's motives and develop a grudging respect.