The hot system refers to structures in our brain that handle fight, flight, and dissociation. It's there for a good reason: to handle emergencies. It's an adaptive system, which in a nutshell means it helps us survive. Most animals have this system as it helps us avoid being eaten. When we're traumatized, its the hot system that experiences it because the cool system is switched off.
The cool system is our normal non-emergency state. We see, hear, and touch things, interact with people, go to movies. Normal experience is handled by the cool system, which stores memories that we can recall later.
The hot system doesn't record memories, just emotional / physical states. So when we're triggered, the hot system kicks in, and we find ourselves dissociating, having a flashback, etc. Since the memory recorder was off, we can't recall the memories of the trauma very well if at all, just the terror and so on.
Here's an article on the subject. It's academic and much of it will sail right over the heads of us regular people, but that said, its not as bad as many:
Metcalfe, Janet and W.J. Jacobs. “A ‘Hot-System/Cool-System’ View of Memory Under Stress,” PTSD Research Quarterly 7:2, Spring 1996.
http://www.ptsd.va.gov/professional/newsletters/research-quarterly/V7N2.pdf