Given repo Foo and repo Bar. I want to merge Bar with Foo, but only into a separate branch, called baz.
git switch -c baz <= put the Bar repo here.
You can't merge a repository into a branch. You can merge a branch from another repository into a branch in your local repository.
Assuming that you have two repositories, base-repo and other-repo, where you want to merge other-repo into base-repo:
Change into the base-repo repository:
$ cd base-repo
Add the other-repo repository as a remote and fetch it:
$ git remote add other-repo git@github.com:xxx/other-repo.git # or use a path like ../foo if you have it locally on your machine
$ git remote update
Create a new branch base-with-other in the base-repo based on whatever your current branch is:
$ git switch -c base-with-other # choose any branch name you want and put it after -c
Merge branch somebranch from the other-repo into the current branch:
$ git merge --allow-unrelated-histories other-repo/somebranch
(--allow-unrelated-histories is not required prior to git version 2.9)