Multiverse stories are most easily told when in the mindset of doing exploratory work in what others have already made than actually making up whole worlds and universes on the fly, though I very strongly recommend making original universes of your own than just playing off of the creativity of others and trying to call that ‘original’. As long as you pay credit where credit is due, it should be fine. But overall, I’d be careful when treading on the storylines of others. People can get fairly sensitive about that, no matter if the story you’ve written is actually good or not.
I personally have been toying around with this idea for a while, actually, though for me it doesn’t just stay in fandom, it would also cross over to other fandoms and the AUs within those fandoms. I’ve written a few first drafts of the first parts of the first adventures, but nothing really set in stone as of yet (aside from the main characters I want to use).
Really, though, I’d just like to see this done by someone, doesn’t have to be me. I’d be more happy to read a multiversal story written by someone else than write one up myself. I just want to see it done.