As a writer of Alternate universes, this one is bound to happen. So lets get started.

Alternate universe has a lot freedom and a lot of restrictions. What? They are still restricted by copyright. Other restrictions include physics, the nature of the characters, and the possibility of how. These are just a few.

But they also give a writer's freedom to play with their characters. This can play into the first idea: The non-canon story.

Many writers have already did this. But I have to empathize this as it is a part of the category. These stories are not part of the main story. Therefore a lot of play room and story ideas. But the characters personality is mostly there. Alliances and rules of the world may change, the character is still the character.

Another idea is the Alternate protagonist. This character is telling or retelling through the eyes of this character. Events happen but how it is done is changed. If done properly, this story will be as interesting as the canon story. Perhaps becoming a canon story.

Yet another but the route I chosen was the multiple universe each play out similar stories. This is a pattern of which you must be careful. Your story for each universe must have a reasonable plot when you mention it. After all, I did this involving at least two universes each with a story and plot. Their plots collide.

Wanting a hard one to do? Boy I got one. Try a plot where characters enters another to change the fate of the second. Remember! Once the characters enter, the main plot idea is there. But details might change even to the point of a different and sometimes unwanted ending. Having an ending different than the main character expected is nice but you must give a reason why. Not having one, robs the reader of a conclusion that in their minds seem more reasonable and perhaps turn them away from any future stories.

Whatever path you choose, may you find success in your efforts.