Well, it could be a story where a TARDIS malfunction lands Doctor Who in the middle of an Avengers battle, and they have to work together to figure out how to get the Doctor back on track and save the day. Or perhaps there's a multiverse crossover where alternate versions of both teams meet and have to face a common enemy.
You could imagine a scenario where Doctor Who and The Avengers team up to save the universe from a time-traveling threat. Maybe there's a villain manipulating timelines, and both teams need to combine their skills and knowledge to stop them.