Shut down the dilithium crystals, you shut down the warp drive and the warp power it feeds into the ship EPS by starving the M/AM reaction of AM fuel. Turn it on full blast into the warp engines with no antimatter bypass control (TWS), you need to burn it as fast as you can or you blow up due to the excess AM build-up in the reactors. Cut off the AM to the crystal, the crystal shuts down and no more AM is made to blow you up. You don't want to shutdown the matter fuel side or you blow up since it is needed to burn the residual AM still in the system. I think I just solved the sabotage scenario in
That Which Survives!
Yeah, I think a variation of this
idea was being thrown around last year in
@TIN_MAN's thread on the
Antimatter Converter Assembly. TOS leaned heavily on the power of lithium/dilithium crystals.
It seems illogical, at least in a dramatic sense, for the most powerful part of the Enterprise to be a small side room when there is a huge something else right nearby that connects all major parts of the ship.
Maybe, maybe not... the small side room made dramatic sense in TWOK to go into and fix the mains. The status of the crystals were dramatically important to the ship's capability in "Mudd's Women", "The Alternative Factor", "The Paradise Syndrome", and "Elaan of Troyus". Yes, the warp drive and it's related systems are huge but the magic is with the dilithium crystals.
I fail to see how there is any evidence that the blue/grey swirly thing ISN'T an Intermix Shaft, or an Energizer, or both, and until now, I thought you and I agreed about that.
I think there was partial agreement. (And that's okay since we don't have to agree as long as it's a good discussion

) There isn't any evidence as to what the swirly energy shaft thing is called but we can try to describe it based on some definitions:
"Energizer" - a device that supplies energy + connection with dilithium crystals
"Intermix" - to become mixed together (as in matter and antimatter)
"Conduit" - a channel through which something is conveyed
"Circuit" - a complete path of an electric current or energy, including usually the source of electrical energy
Does the swirly shaft thing supply energy and is it connected to the dilithium crystals?
Partially as I think it does since it appears to run energy from the bottom upwards and back towards the warp nacelles but the crystals aren't visible in TMP and are in a side room in TWOK.
Does the swirly shaft thing contain matter and antimatter mixed together?
Doubtful - this is because if they are *mixed together* the matter and antimatter will have annihilated each other. Intermix really belongs to the Matter-Antimatter Reaction Chamber ("That Which Survives")
Does the swirly shaft thing appear to be channeling something?
Yes, swirly energy 
Does the swirly shaft thing appear to be a path of energy, including the source of it?
Yes, if we count what appears to be the source at the bottom of the shaft.
I'm just trying to follow the thread and find an actual location in the ship for 2(+) Engine Rooms, and hoping that determining the function of a given prop might help. The refit designs in that book do a good job of this, and my goal was to try to apply something similar to TOS.
Is there any reason you can't use the curved corridor or the DOTD exit as cues for where the engine rooms are?
The problem with using books like "Mr Scott's Guide to the Enterprise", "FJ's Technical Manual", and cutaways like Kimble's Enterprise is that rarely do they match up to anything seen on screen which is problematic. If they are not adhering to the source material they just only serve to muddy up the waters even more, IMHO.
Maybe the Energizer room in "The Alternative Factor" doesn't back right up to the orange structure or be located right underneath the syncrotron, thus one or the other is the Energizer?
Same notation, but from FJSTM this time. And, since a syncrotron accelerates particles, if there is a crystal in there and energy is moving through it or from it, which seems to be the case at times, syncrotron is as good a word as any.
If a "syncrotron" accelerates *particles* and dilithium crystals charge and discharge *energy* then that just doesn't sound right. Particles contain energy but dilithium crystals don't deal with particles - at least not the TOS crystals. Only the TNG dilithium crystals do that when they *regulate* matter and antimatter reactions. "Syncotron" isn't a good fit, IMHO. That's probably why I like the vague "DTD"
The DTD is probably the top or somehow connected to an energizer since crystals are later contained in it (Season 3).