Quake 3 models are one piece for the body, and one piece for the head. Doom 3 models are one piece total, from what I’ve seen.
To do what you’re asking, you would need to follow these steps:
Download an .MD3 format importer/exporter for your modelling package. (For Quake 3 stuff, I prefer pop-n-fresh’s md3 plugin for 3dsmax.)
Import the model into your modelling program, and export it as an .OBJ file. For 3dsmax, you’ll need an OBJ importer/exporter.
Import the .OBJ file into ZBrush and detail it as you wish.
Export from ZBrush the detailed model as an .OBJ file.
Import it back into your modelling program and optimize the polygons until they’re at a good count. A decent number for today’s computers would be anywhere from 2,000 to 4,000 polys. Some Doom 3 models use less and some use more. Just get it to look right, and make sure the model is symmetrical so you can animate it easier.
Use your favorite normal mapping plugin to generate the normal map from the high poly model.
Rig the low poly model, and animate it.
The toolset for Doom 3 has not been released yet, therefor there is no information as to the animation frames, methods, etc. to get to the final result. Wait a few weeks for the SDK to be released, and they’ll probably explain everything.
To get the model into Doom 3, you’ll need an .MD5 exporter, and currently there are only third-party plugins for this. I would personally wait until the official stuff has been released.