The problem you are having seems very similar to one I was experiencing a few months ago.
What happened was the plugin edited some of my scripts that I had made and added a random comment to them, which happened to hide require scripts inside of it that couldn’t be read (this would explain why the problem still occurs when the plugins have been deleted).
Please check out this person’s post as it may be a solution: Backdoor hidden inside text unreadable by the ROBLOX editor.
Also, are you getting any strange things in Output, such as requests to turn on API services?