The end of the game. Of course, once you succeed, everyone has to go about their lives. Thus, the Ultimate Alliance is disbanded. The reactions of Spider-Man and Wolverine really show that over the adventure the team has become close friends.
In the second game when Nick Fury asks for the heroes' help in disabling the bombs that Venom and Green Goblin set up, if the player chooses the "Diplomatic" response (where the characters basically say, "Alright, let's see them, but no tricks this time, Fury"), Fury's response will be a quick but completely genuine, "I knew I could count on ya."