I was recently reading about George Eliot’s Middlemarch that it started its life as two separate books, one about the townspeople of Middlemarch and another about the folks in the countryside. Eliot couldn’t figure out what to do with either book until she hit upon the idea of knitting them together. The result is a book with a handful of separate storylines that touch each other mostly incidentally and thematically, but nevertheless form a coherent whole.
The novel I am working on has a similar (though less sweeping) structure. The two main characters know each other and have some history; they have a few important scenes together; but mostly their stories are separate, parallel, and complementary, united by the book’s theme.
So, while I’ve never been in the position you’re in, I think you can look around to other stories for inspiration. Is there another story you want to tell that is thematically related? Maybe you can develop another character, connect her to your existing characters in various ways, and weave her complementary story through your existing storyline.