You wind up writing two stories. The only reasonable approach is to make the stories intersect in a way that completes both of them. What pops into my head is a he-she meet-cute where the action at that point highlights both of their problems.
Every story revolves around resolving a conflict.
Their conflicts have no intersection other than a plot-collision that (oh, this is good!) puts them in opposition to each other.
Over time resolving these two unconnected conflicts gives you the chance to make the two resolutions somehow require that they work together.
If you can’t write act three after that, don’t call me!