"The X in the File" is episode eleven of season five of Bones, the forensic drama television series loosely based on the novels and life of anthropologist Kathy Reichs. In this episode, the body of a suspected alien is found in the New Mexico desert.
Aliens in the Desert
This episode opens in Roswell, New Mexico, at night, with a man on the phone to his wife, telling her that he's done hunting aliens and he's in his hotel room in Florida, working late. Clearly he's being economical with the truth. Then he sees something - a body in silvery clothing. A body that, even in the state it's in, doesn't look human. Only humanoid (guess what the title is referencing). Then he hears something and, thinking it's aliens, turns around. He sees a pair of glowing eyes. Then several pairs. At which point he runs away.
A Real, Live Alien?
In New Mexico, Booth is excited at the idea of finding a real alien. Brennan asks if he means one that has come across the border from Mexico. She agrees that there is a good chance that there are aliens out there, but that they would have sufficient intelligence not to die in the middle of the desert. Which, going by the behaviour of supposedly intelligent humans, is perhaps not a given.
The Body is Human - Of Course
Brennan quickly identifies the body as being female. Human female. She wants the body shipped to the Jeffersonian, but the local sheriff doesn't agree. He says that, unless he gives the FBI jurisdiction, they have to go through a legal process to get the body. He's not being awkward for its own sake; he doesn't want to be accused of shipping an alien body off to Washington for secret testing. Which has happened before. Even though Brennan says the remains are not extraterrestrial. He wants the help though. Then a very familiar theme tune starts playing (again, the clue is in the title), but it's only a mobile. It belongs to the man who found the body.
An Autopsy in a Spooky Deserted Hospital
So, they have to do the autopsy in a deserted part of the hospital which got shut down. Booth doesn't fancy being in the spooky hospital with the dead alien; Brennan is okay. They can send samples and the coat to the Jeffersonian, but not the body. Said body, other than being dead, belongs to someone in very good health, and surprisingly in one piece. Scavengers would normally have had a field day, given it's been in the desert for a couple of weeks. Booth gets to interview the man who found the body. Who says that he was abducted by aliens.
Flesh is Not Brennan's Thing
The examination of the body in an MRI causes the body to sit up. Although that's because the skull has several ball bearings in it. Still rather weird to see. The body is definitely human, and is that of another alien hunter. The case brings in a lot of UFOlogists, of the crazy sort. With the body remaining in New Mexico, Brennan has to work with flesh. Flesh is not her thing. The dead body is unlikely to have anything to do with real aliens - even though she has a video of what looks like an alien spaceship surrounded by humans in hazmat suits.