If you don't want to go through each page, you would have to use something like MassCategorization and remove the category from the pages shown on the category page.

^... which will only work if the categories are added directly and not through a template.

For pages not to appear in a category, regardless of whether the category page exists or not, the category has to be removed from every page. Either manually or with the script linked above, if applicable.

How do I download this tool? I'm new to admin roles, so I'm kinda needing some stepping stones for now.

You don't download it, you import it to your global or local js. Assuming you're talking about the Herois wiki, you should use the following code in your common.js:

importArticles({
    type: 'script',
    articles: [
        'u:dev:MediaWiki:MassCategorization/code.js',
    ]
});

Make sure to turn on personal js in preferences.

For some reason, I can't edit common.js, even though I am an admin there. How do I unlock this page.

Did you click the link I sent? You should be able to edit it since it's your personal js, not the wiki's common.js.

Alright. I figured it out and I downloaded it. How do I use it to delete categories?

Go to a category -> open the tool bar -> click mass categorization -> go to mode and change it to remove -> click "Add category contents" -> add category you want removed -> click OK -> click Start

Read the documentation

Alright, I picked it up. Thanks for the help, guys.