Git refusing to merge unrelated histories

The default behavior has changed since git 2.9:

“git merge” used to allow merging two branches that have no common base by default, which led to a brand new history of an existing project created and then get pulled by an unsuspecting maintainer, which allowed an unnecessary parallel history merged into the existing project. The command has been taught not to allow this by default, with an escape hatch --allow-unrelated-histories option to be used in a rare event that merges histories of two projects that started their lives independently.

See the git release changelog for more information.

You can use --allow-unrelated-histories to force the merge to happen.