Thanks to wsippel for pointing this out.
Metroid Prime runs on a very heavily modified version of Unreal Engine 2. You can certify this to yourself by looking at the text box next to Asset_CMDL_EditorModel. Notice the word "/cooked/" in there.
For those of you who have worked with the Unreal Engine, you'll know what this is, else, you might wanna read. Cooking is a term for compiling all of the maps, scripts, materials, etc. you've made into one usable executable, or "game". It was used primarily for consoles, although now support has come out for PC cooking, resulting in faster loading times.
They also used Unreal's level streaming feature. This is highly detailed in Unreal Engine 3, but was also present in 2. It's funny how Retro got a private license for this stuff yet never sought to bring it out.
I also can confirm some UnrealScript source files exist on disk, which I am attempting to extract. Will probably branch this off into a separate thread for loads of fun and wackiness.