Spider Wars, Chapter 2: Farewell Spider-Man - S5-E13
Character mistake: When Stan Lee is asking Spider-Man what he plans to do after saving all of reality, he responds by saying to find the real Mary Jane. Moments later in the final scene, Madame Web tells Spider-Man that she is taking him to find the real Mary Jane, which elicits an incredulous response from Spider-Man, as if he didn't know that was already the plan.
Answer: Yes. Many things that would have been in the sixth season would have had Norman Osborne returning from limbo and reclaiming the title of the Green Goblin, Richard Fisk, the son of "The Kingpin" Wilson Fisk would return as a crime lord known as "The Rose", Ghost Rider would have appeared to help Spider-Man stop Dormammu from returning to Earth and Madame Web and Spider-Man would rescue Mary Jane from limbo.