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Have you tried reading the documentation (https://www.akeeba.com/documentation/admin-tools-joomla.html)? I have documented all of that there.

Go to Admin Tools, Web Application Firewall, Configure WAF, Basic Features and set “Defend against plugin deactivation” to No.  You can now disable the System - Admin Tools plugin just fine.

Documentation reference: https://www.akeeba.com/documentation/admin-tools-joomla/web-application-firewall.html#waf-configure-basic-protection and https://www.akeeba.com/documentation/admin-tools-joomla/system-plugin.html

If you had used the Administrator Password Protection feature you can either turn it off (Admin Tools, Password-protect Administrator, Remove Password Protection) or delete the files administrator/.htaccess and administrator/.htpasswd — that's what the Remove Password Protection button actually does.

Documentation reference: https://www.akeeba.com/documentation/admin-tools-joomla/admin-pw-protection.html

If you are using the .htaccess Maker and you want to revert back to the default Joomla .htaccess file you need to replace its contents with the contents of Joomla's htaccess.txt file. Note that the documentation tells you to turn off all options and use the Save & Create .htaccess file which, as it says, is the same as using the htaccess.txt content, but this is a bit too drastic for your particular use case (you don't want to lose your configuration).

Documentation reference: https://www.akeeba.com/documentation/admin-tools-joomla/htaccess-maker.html

That's it, really. Removing / replacing the .htaccess files and disabling the system plugin undoes all changes made by Admin Tools and disables Admin Tools' code which would run on every request. You are “shields down”, as they'd say in Star Trek.

To go back to “shields up” revert the changes you made in the reverse order you disabled them: first the .htaccess Maker (if you were using it), the the administrator password protection (if you were using it), then publish the system plugin, and finally set “Defend against plugin deactivation” to Yes.

I strongly recommend keeping a log of the changes you made and the reason you made them so when the time comes to undo them you don't have to rely on your recollection. If that sounds obvious to you, please don't take offence; remember that I don't know your skill level and I am used to helping people who are stressed, frustrated, and likely to start making changes they won't remember unless I remind them to take note of what they are doing.