I’d like to set a first-person game underwater. I was wondering which scripts I should be editing. The character motor? The first person controller? Also, where do I start changing all of this?
The Character system is not what you want. All of them are designed for above-water applications. What I would do is use a RigidBody with gravity turned off, and apply forces to it. Remember to put it in a high drag situation.
If you have Unity pro, you can also do some clever stuff with post-processing.