I would commit your working directory to ensure that it exists in history before fetching. (ensure you are in the projects root folder)
git init
git add -A
git commit -m "my latest'
now we have it
git remote add origin url-to-your-remote
git fetch origin
now we have the history from the remote
git reset origin/master
now our current commit is the latest from the remote
git add -A
git commit -m "Committed my state"
now we use our current working directory as the snapshot for the next commit.
git push -u origin master
push up your changes and track the branch.
the key is the reset command with no --hard option. It keeps your working folder the same while pointing the branch to what you got from the remote.