I am using a Dedicated Server. In the web-hosting side, I have folders arranged like so.

html
    forum
        files
    images
        files
    Equinox
        index.php
        header.php
        footer.php
    style
        style.css
    mc-multiplayer
        style
            style.css
        index.php
        header.php
        footer.php

I am trying to get the index.php of mc-multiplayer to link to the css file in mc-multiplayer, but no matter what it keeps going to the style.css file in the html folder.

Show how you include your css.

It would be helpful to see your code so we could tell you what you're doing wrong. However, the correct element to use in html/mc-multiplayer/index.php or html/mc-multiplayer/header.php (where I assume your link tag would really be) should be

<link rel="stylesheet" type="text/css" href="style/style.css />

You're not using a <base> tag, are you?

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