It's advised to run the repair program in Safe Mode with Networking so that your antivirus program doesn't block any aspect of it.
I'm not sure if the program would help with your problem though.
Windows does have its own repair tools depending upon which version of Windows you are using.
I'm going to assume that you are using Win 10, so open a Command Prompt (Admin) and enter these cmds to see if they resolve anything.
They will all take a while to run before they give their report.
dism /online /cleanup-image /startcomponentcleanup
dism /online /cleanup-image /restorehealth
sfc /scannow
exit
Note the space before each /
If you are still unable to boot into Safe Mode or use your machine normally, then again assuming you are using Win 10, you will need to create Win 10 install media after reading the instructions at
https://www.microsoft.com/en-gb/software-download/windows10 to perform a repair install which won't affect your personal stuff or installed programs.
When you've done that, open Windows/File Explorer - This PC - insert the install media and double click on its drive.
This will start the process if using a DVD but will open to its files if using an USB where you would then double click on setup.exe Application.