Add plugin
The way that you can add custom plugins to the mix, is by adding them before or after a built-in plugin.
Let's say we want to use the "remark-github-alerts" plugin. It must be added before or after a built-in remark plugin. Do the same with rehype plugins too. Let's say we want to add it after the built-in "remark-gfm" plugin.
Something like "remark-github-alerts" is already built-in.
NOTE
It doesn't matter if the built-in plugin is disabled, the custom plugin added by you will work.