The new story in Marvel Puzzle Quest could potentially offer fresh plot twists. It may explore a different corner of the Marvel multiverse, bringing in alternate versions of characters. There could be new quests that are tied to the story's progression, and as the story unfolds, it might unlock exclusive rewards for players who complete certain parts of it. This new story could also be a way to integrate some of the more recent Marvel comic or movie storylines into the game, making it more relevant and exciting for fans.