Gameboy emulation

For Pokemon play, one uses an emulator on the PC or other computer (or, you know, you buy an actual Gameboy, but I'm assuming you're more interesting than that).  Mostly that's VBA or VBA-M, although there are others. On Win64, VBA-M is not working for me with Pokemon Emerald, so I'm using a 32-bit VBA, but the source tree for VBA-M is on SourceForge here.

Clearly, part of this is the emulator itself and part is the UI and associated tools, so we've got to tease those threads apart. But I'm most interested in how the ROM itself works (i.e. its file structure and how all that stuff is defined). It appears to be programmed on this virtual machine in a bytecode; how does that work, and how can we pull it apart to build a new ROM or modified one? I'm pretty sure the emulator code itself is going to tell us that, but the documentation is horrible, all read-the-code-Luke with a few cryptic comments for things the authors found tricky or unexpected, I'm assuming bug fixes mostly.

Anyway, the reason Pokemon is suddenly featuring on this heretofore more general blog is that my son has a truly fascinating idea for a programming project involving emulated Pokemon. More here later if it proves feasible to do what he wants to do. But in the meantime we gotta understand and clean up this codebase, so it's code understanding to the forefront!