Well, usually they have lots of alternate realities and characters jumping between them. The plot often involves saving or changing multiple universes.
A clich茅 multiverse story often has characters discovering their ability to travel between universes by some random event. Also, there's usually a big threat that spans across multiple realities and the hero has to fix it all. Plus, there might be some confusion about which reality is the 'true' one.
Commonly, in a clich茅 multiverse story, you'll find complex timelines, characters with multiple versions in different universes, and a convoluted plot to keep track of. It might also have some kind of device or power that enables the multiverse travel, and a lot of 'what if' scenarios explored.