After recently being diagnosed with Narcolepsy with Cataplexy, and put on Provigil, I did some research on the condition. Research has found that narcolepsy is caused by the lack of two related brain chemicals called "hypocretin-1" and "hypocretin-2"
http://med.stanford.edu/school/Psychiatry/narcolepsy/faq1.html#1
The absence of these two chemical disturb the individual's sleep pattern causing them to almost immediately to into REM sleep bypassing the Non-REM stage. The cause of the low levels of the brain chemicals is unknown but researchers have found that people with narcolepsy often have an antigen called HLA-DQB1*0602 present in their white blood cells. HLA markers are often found in people who have auto immune diseases such as juvenile diabetes, ceiliac diseases, and muscular dystrophy. While the presence of HLA is not a definite diagnosis of narcolepsy, it is thought that it is a predisposing condition. It is possible that, as in other autoimmune conditions, the body is attacking its own cells, and in this case it is the hypocretin-1 and hypocretin-2 being destroyed.
Since multiple autoimmune diseases, called Multiple Autoimmune Syndrome, often develop within the same patient, if you are having sleep issues and have been diagnosed with another, or other, autoimmunes, let your doctor know. Like other autoimmunes, there is no cure for narcolepsy but treatment is available.