There was an old, old mod, I think Chris Jones had a hand in it; based on the old AGT game universe switching system by Lansing and a couple of others I think. It has a TOS mod in it and it had its own FX in terms of sound effects, music, weapon textures, etc. It might be available still in Ghost's Fleetdock 13. If not, PM me.
Oh, EDIT: this mod was originally made for SFC 1!!