System plugins run on every page request, before and after the rest of the page is assembled. Rather than affecting one article or one component, they change how the site as a whole behaves — how URLs are formed, what is cached, what security headers are sent, what gets logged.
A few of the system plugins that ship with Joomla:
- SEF — rewrites links into search engine friendly URLs.
- Remember Me — adds the "remember me" option to the login form.
- Cache — serves cached pages to guests to cut down on server work.
- Redirect — works with the Redirects component to catch broken incoming links and send visitors to the right page.
- Fields — makes custom fields available on articles, contacts and user accounts.
- HTTP Headers — sets security headers such as the Content Security Policy.
- Debug — reports database queries, timings and language diagnostics while a site is being built.
Which of them are enabled differs from site to site. The full list, and the settings for each, is in the administrator under System → Plugins, filtered to the system type.