Most of the game is implemented in C++ and only accessible through the game's executable (.exe file). Fortunately, RED4ext and Cyber Engine Tweaks hook into that, and Codeware provides and extends a common interface for both.
The hooks are dependent on binary addresses, which is why the core mods are version dependent (and why cracked games don't mod well).
Scripts
Scripts are precompiled into r6/cache/final.redscripts . As the file extension suggests, they can be modded with redscript.
The tweak database
Any properties of game items and characters are defined in the tweak database. You can learn more about it under Material: interlinking -> Tweaks