When it came time to pull things together, we thought it'd be fun to try and maintain the histories. So I added his repo as a remote and simply merged his unrelated history into mine.
Fast forward and now we offer hoodies as swag to anyone who contributes to the repo. We personalize the hoodie with your git username, the truncated commit hash of your first commit, and the number of parent commits to your first commit.
Having 2 root commits means that both my cofounder and I have hoodies with a large 0 as number of parent commits. Just a nice way to commemorate this accident of history :)