In my idea, the mutants discover the history of the Gems, and how the two factions are related. The Cluster and its prototypes are gathered by beings like Charles and Lehnsheer and fixed back together by a concoction made out of recovered Gem energies, stem cells, and the liquids that allow people to gain healing factor characteristics that are re-modified so that beings with the concoction in their systems can heal faster than they're damaged, regardless of their damage size. New gems like Emerald, who's gemstone is on the outside skin of where her heart should be and possesses the power to control plants, forests, jungles, etc. come along. Steven and Connie are tested with the concoction by Charles and Lehnsheer, with Peridot and Lapis watching the whole thing. They now have healing factors like Logan does.
The X-Men and the Crystal Gems become friends, and the Gems are washed with the concoction as well. Mutants also wash themselves for the ability of weapon summoning. They face entities like En Sabah Nur, who goes by "Apocalypse", and many others to protect the world. In this one, the X-Men are respected by democracies like the U.K., Canada, Australia, and the U.S. But I could probably save that for later. I ALSO have a concept fully like this, but based entirely on X-Men: Days of Future Past. I just need to decide the years these events take place. No one knows the exact years of the SU franchise events, so I might need some help.