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

The reason behind this is that 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.

More information can be found in this answer.

I ended in the same situation after a series of mishapps. Have a look at this thread : I just did a 

git pull --allow-unrelated-histories

and it was fixed!

The "fatal: refusing to merge unrelated histories" error in Git occurs when you try to merge two branches that do not share a common commit history. This scenario often arises in situations such as: Merging Two Independent Repositories: This happens when you attempt to merge two completely separate projects (repositories) that started their lives independently of each other, without any shared history. Repository Reinitialization: If a repository was re-initialized (i.e., started afresh with a new git init command) but needs to pull or merge changes from a backup or a previous repository state, the histories would be seen as unrelated. Squashed or Rebased Commits: If the history of one branch has been rewritten (for example, through rebasing or squashing commits), Git may fail to recognize the related history that it once shared with another branch. How Git Handles Histories Git is meticulous about tracking the lineage of commits for integrity and version control purposes. Each commit in a Git repository has a parent commit (except for the very first one), creating a chain that traces back to the initial commit. When you attempt to merge two branches, Git looks for a common base commit to correctly integrate the changes from each branch. Without this common commit, Git cannot safely perform the merge as it cannot ascertain how the changes from the two histories should interact.