The scripts are written a C++-like DSL, and are part of the assets. There's map scripts, weapon scripts, AI scripts etc. They process high-level triggers and events to handle the storyline, different behaviours, and so on.

So you could make a magical weapon writing just scripts, for example. But yes there is a limit in the flexibility, if you want to make a completely different kind of game you probably have to change the C++ classes as well...