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."
In the first game, one of the optional objectives is destroying Galactus' Optronic Drills to save the Skrull Planet from being eaten. While saving worlds is a given for superheroes, the Skrull are known enemies of Earth and a good majority of them make up the enemies on Skrull Planet, attacking the heroes on-sight. But despite this, alongside the Skrull Empress tricking the heroes earlier and Nick Fury pointing out that the Skrull will still be hostile when destroying the Optronic Drills, the heroes state that they would help the Skrull whether they want it or not. And accomplishing this optional objective is well rewarded in the ending as the Skrull forms a partnership with Earth and come to its aid when the Kree attempts to enslave humanity.