How do you apply mods to Jedi knight Jedi outcast

Mods are usually contained within a .pk3 file. This file should not be expanded, but placed into your base Jedi Knight II/Gamedata/Base folder.
If the file is not a .pk3 file, but a folder containing other files, then this folder should be placed in your Jedi Knight II/Gamedata folder, but the Base folder.