Science File Information:
When Scully finds Mulder shivering in a bathtub in a hotel room, he is exhibiting symptoms of shock. People go into shock when something happens to the body that impairs the heart's ability to pump blood. It could be triggered by a physical injury, such as a massive loss of blood that weakens the flow of blood to the heart itself, or a chemical influence in the bloodstream (a drug) that dialates the blood vessels and makes it harder for the heart to push blood to the rest of the body. Although Mulder is covered with blood at the beginning of the episode, it's not quite clear which form of shock he might be suffering.
To get a more thorough explanation of shock, read the Encyclopaedia
Britannica entry on the condition at http://www.britannica.com/bcom/eb/article/7/0,5716,69207+1,00.html.
To learn how to treat shock victims, swing by WebMD's page on the subject at http://my.webmd.com/content/dmk/dmk_article_1459405.
As the agents try to piece together the events of the past few days, Mulder suffers from severe headaches, accompanied by vivid flashbacks to his early childhood. Scully thinks that Mulder may be suffering from Waxman-Geschwind syndrome, a grouping of behavioral traits that is believed to accompany some cases of epilepsy (which I'll explain in a moment). According to Scully, Russian author Fyodor Dovstoyevsky suffered from this rare affliction.
To read about Waxman-Geschwind syndrome, read Robert Finn's review of Eve LaPlante's book Seized at http://www.nasw.org/finn/brnstrm.html that discusses the nature of WGS.
Scully suspects Mulder has been framed somehow, and lab work performed on a sample of his blood supports her theory. Floating around in Mulder's bloodstream are traces of ketamine, a fast-acting veterinary anesthetic. In small doses it is purported to give humans vivid hallucinations, much like the drug LSD. However its connection to Waxman-Geschwind syndrome and epilepsy is a little closer than one might expect. As I understand it, all three are tied to an amino acid in the brain called glutamate. Glutamate, like its cousins seratonin and acetylcholine (see ICE and SLEEPLESS) is a neurotransmitter, a chemical found in neurons, or nerve cells, that is used to send signals from one neuron to another. When someone has a form of epilepsy called complex partial seizure disorder (also known as temporal lobe epilepsy or TLE), the temporal lobes of the brain produce too much glutamate and the neurons go into signal-passing overdrive. This causes a condition called excitotoxicity--in essence the neurons get hyperactive, generating a veritable electrical storm of brain activity, and they burn themselves out. Waxman-Geschwind syndrome is often the result of this phenomenon; sufferers of WGS have periods of artistic brilliance in between bouts of depression and delerium as their temporal lobes fritter away.
So where does ketamine figure into all of this? Ketamine supposedly acts as a buffer, altering chemicals in the brain to allow the glutamate rush of excited neurons, while staving off the excitotoxicity that occurs in TLE. (Unfortunately, doctors and scientists still don't know for sure what exactly ketamine does, or what long-term effects it might have on people, so this theory is just that--a theory.) Using this explanation, it might make sense for Mulder to suffer from a mental disorder usually associated with epilepsy--yet conveniently have the disorder cease with the end of the episode.
The above is most likely a vast an oversimplification of how things really work. For a great site that puts neuroscience in layman's terms without dumbing it down, go to "Neuroscience for Kids" at http://faculty.washington.edu/chudler/neurok.html.
To read a good graphical primer on neurons, neurotransmitters, and how drugs affect them both, go to http://www.utexas.edu/research/asrec/addiction.html.
If you'd like to know more about ketamine, there are many resources on it on the internet, including a TIME Magazine article at http://www.pathfinder.com/time/magazine/1997/dom/ 971020/behavior.is_your_kid_o.html and a British fact sheet found at http://area51.upsu.plym.ac.uk/infoserv/drugs/graphical/grphket.html.
As it turns out, Mulder has been a patient of a local doctor who's been experimenting with a not-quite-orthodox treatment to help people recover their memories. Not only does Dr. Goldstein administer a mild dosage of ketamine, he's giving the neuron excitation a little bit of a jumpstart by stimulating the patient's dura mater with electricity. The dura mater is the outer meninges of the brain, a layer of membrane that sits between the skull and the brain itself, cushioning a person's fragile gray matter. Its name literally translates to "tough mother." (And who says scientists don't have senses of humor?)
To see for yourself what the dura mater looks like, check out Virtual Hospital's brain dissection page on dura mater at http://www.vh.org/Providers/Textbooks/BrainAnatomy/ Ch2Text/Section04.html.
The Mad Scientist Network has some more background information on the different layers of the meninges (to include dura mater) at http://www.madsci.org/posts/archives/feb98/884706981.An.r.html.
Mulder is convinced that the memories he's experiencing are real, but he's probably being a little hasty with that conclusion. Scientists have found that memories aren't always trustworthy, even without a hallucinogenic anesthetic in your veins and a electric probe thrust through your skull. San Francisco's Exploratorium museum has a whole exhibit devoted to the science of memory, including a few experiments you can try on yourself.
Don't forget to check out the Exploratorium's Memory exhibit, especially the experiment mentioned above: http://www.exploratorium.edu/memory/messingwithyourmind/.
Learning about memory itself is interesting, but what exactly happens in the brain when you remember something? BBC News reports on some University of Geneva scientists who were able to photograph the formation of a memory at http://news.bbc.co.uk/hi/english/sci/tech/newsid_528000/528617.stm.