So, what is the "energy" in the glowing tubes? Probably a plasma system. Now, is the plasma itself consumed as a fuel source needing continuous replacement (open system), or is it a closed system where the plasma is "energized" (in the main energizer maybe?) and the electrical and/or subatomic particle charge is removed at the energy using equipment/systems, so, the M/AM reaction just charges up the plasma which is not consumed. TNG clearly uses the later scheme, so, why not TOS. TNG calls it "warp plasma" which is probably some treknobabble substance that can transport electrical as well as concentrated subatomic particles to the warp engines or convert it into simple electricity (probably transported in the ship's EPS.) YMMV So, when the main energizers are down (as in The Doomsday Machine), the ship lost the ability to provide warp power to the warp engines, thus, loosing warp drive. (Same with WNMHGB and Mudd's Women and maybe the worry in The Alternative Factor.) The engines themselves weren't damaged, only the energizers or the dilithium crystals. Use of impulse power can be directed into the warp engines to create a strong gravity field around the ship (not powerful enough to create a warp field threshold) that allows the impulse engines to generate low-FLT speeds without a warp effect. Of course, the ship burns its impulse fuel supply very quickly. This is also probably the power system on the Romulan ship in Balance of Terror. It all fits very nicely.