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Nasal cavity
Yet another handy body part. Not only can it be used for breathing, but the nasal cavity also doubles as a useful storage spot for alien implants. 
Nasal Pharyngeal Tumor
Scully was diagnosed with cancer in the episode Memento Mori when it was discovered she had a cancerous mass in her nose, between the superior conchea and the sinoidal sinus. The tumor is inoperable, and treatment is "difficult, to the extreme" to treat as the tumor is on the wall between the sinus and the brain. Scully's nose-bleeds appear to be a symptom of her cancer, which now seems to be cured after the radical treatment suggested by Cancerman (of all people!) in Redux II. (J Foster) 
It was the Navajo desert which held secrets from US government experiments being conducted by Access Power scientists after the second World War. A boxcar, containing the bodies of alien-human hybrids with smallpox vaccination scars, was uncovered by Native American Eric Hosteen in the Anasazi trilogy. Cigarette Smoking Man later ordered that the boxcar be burnt, as Mulder had discovered the bodies. Navajo also refers to the encyrption technique used by the Americans during WWII, when secret documents were written in Navajo - recognizable by the long strings of consonants. If you look closely at the Navajo-encyrpted text on Mulder's computer, you can spot the phrase 'do re mi fa sol la si do'. (thanks to Genevieve Pigeon) 
Near Death Experience (NDE)
The proverbial NDE has become something of a prequesite for appearing as a regular on The X-Files. Scully did it in One Breath, Mulder was off with the fairies during Blessing Way, and Skinner told Mulder all about his own Vietnam-based out of body experience in One Breath. What's it like to have a NDE? Well be prepared for some visits from long lost family members, if Mulder and Scully's own expierences are to be believed. For Scully we had a long black tunnel, and for Mulder a certain Native American motif. (Scarlet Galvan) 
An acronym for the National Investigative Committee of Aerial Phenomena, an organization which investigates government coverups such as Roswell. The venerable Max Fenig was a member of NICAP who first met Mulder when they were both caught near a downed UFO in Townsend, Wisconsin. 
Translated as 'second generation' from its Japanese origins, this word is most often used to describe Japanese-Americans born during the WWII era. In The X-Files, Nisei also refers to the hybrid alien-human 'children' which were the result of experiments by Japanese scientists such as Dr Zama who worked for the US government after the war in the episode of the same name. 
Not everything dies
After the Alien Bount Hunter's rather blunt 'Everything dies,' it was a refreshing change to hear Marita Covarrubius' own rendition: "Not everything dies, Mr Mulder" in Herrenvolk. (Kate Moore)