Plug in Git doesn't add new code to your Shopify theme.
During installation you choose the GitHub repository you want to sync with. This can be an empty repository (recommended) or an existing non-empty repository.
If you choose an existing non-empty repository, the first commit by Plug in Git will remove any files that exist only in git and not in the shop. Of course the history will be preserved so nothing will be permanently deleted.
After choosing the GitHub repository you want to sync with a progress bar will be shown displaying the progress importing your current theme into GitHub.
When this is complete you're installed!