Plugins and scripts are 2 type of code MQ2 can run within your EQ session.
Plugins are written in "full" programming languages (mostly C++), and are must be compiled with other tools before they can be used. Plugins are able to access all the normal things programming languages can, and all the special things mq2 makes available. Script files are not pre-compiled, and so they can be edited and re-run with changes, without being compiled each time. Scripts run a bit slower, and have to be written in the special script language MQ2 provides.
Plugins are often used to add new areas of functionality to MQ2, for example providing a whole new slash command. Scripts use functionality and get EQ to do things using commands.
MQ2 comes with various "core" plugins which provide the starting functionality needed, and then other plugins are available to fit specific needs or interests, or provide other functionality which may or may not be of use to everyone.
MQ2 will generally have a few plugins loaded automatically, and you can then load and run more plugins as you see fit.
You can list the current plugins using the command /plugin list
To load a plugin you need to know the plugin file name - /plugin MQ2Bot would cause MQ2bot plugin to be loaded, and run it's initial code.
/plugin list would now include MQ2Bot in the list of plugins.
/plugin MQ2Bot unload will unload the plugin.
Each plugin can do whatever it needs to. Most often this is adding one or more slash commands to those available in EQ. Unloading the plugin will remove it and any commands or functionality it made available. Since each plugin can do what it needs to, the specific commands, or how to access the functionality the plugin adds, is down to the person writing the plugin. The wiki here lists all the plugins provided and under each plugin entry you can find the details of how that specific plugin functions, what commands it adds, and any requirements it might have to operate properly.
You can cause a plugin to be loaded each time you start MQ2 / EQ, using /plugin name auto"
To use a plugin is easy.
1:start mmoloader/mq2 compile of your choice.
2:start EQ without using the patcher.
3:select a toon and log into game.
4:once in game you can type /plugin mq2(plugin name without the ()). So an example would be /plugin mq2melee
5:some plugins have a UI (user interface) piece, if you get a message saying that the ui piece is loaded but you need to reload your ui, you can just type /reload to reload your ui.
6:read the wiki for slash commands for the plugin you just loaded, some are easy like /melee help.