This episode opens with Agent Scully being interviewed by Section Chief Scott Blevins . He is telling her about her new assignment to work on a project with one Agent Fox Mulder. He asks her has she heard of Mulder and she tells him hesitantly that yes she has heard of him through his reputation as a bit of a weirdo, being into the paranormal and deciding to abandon his promising career in the Violent Crimes Unit to work on the buried X-Files. All the while this is going on Cancer Man is in the background puffing away.
      Scully then goes to meet Mulder in his basement office, as she knocks and enters he says "Noone down here, but the FBI's most unwanted". Once they are introduced Mulder says he knows her work and has read her thesis on rewritting Einstein. Mulder then shows her slides of exsangunated cows corpses and they discuss the possibility of Extra-Terrestrial life, Scully saying she does not believe that aliens are visiting earth, that it would be impossible for that to happen. Mulder however says that she is using convention wisdom to argue her point. Anyway, he tells her about the cases he is interested in connecting across America linked by one thing; the presence of two small red lumps on the victims bodies.
      They then proceed to Bellifleur Oregon to investigate the latest death. The deceased is one Karen Swenson, she also has the red marks on her body. Mulder has the body of another victim in the area exhumed, Ray Soames, to investigate his death also. However, when they do all they find is what turns out to be that corpse of an orangutan. There was a strange metal strip found in the body of the orangutan.
      Mulder and Scully go on to interview two of Karen Swensons high school classmates, only to find them both in a mental hospital after they were in a car accident. Billy Miles is in a vegetated state and Peggy O'Dell is in a wheelchair. Mulder notices that Billy Miles feet have a layer of soil on them, which is mysterious considering he can no longer walk in his current condition. Suddenly Peggy O'Dell starts to throw a fit and in the course of subduing her two red marks like the others are found on her body.
      Mulder and Scully then go to investigate the place where Karen Awenson was killed, only they are told to leave by Detective Miles, Billy's father. They do leave and as they are driving back to there motel there is a blinding flash of light and just before it Mulder had checked his watch. In what seemed a second later the car cuts out and Mulder checks his watch again, he discovers that there are nine minutes missing. He tells Scully that this is a sign associated with sitings of aliens spaceships, Scully however is skeptical. Mulder puts an X in the road to mark the spot and then they drive on again to there motel.
      Mulder and Scully are in their seperate rooms at the motel. Scully is running a bath and getting undressed in the bathroom when she notices two marks on her skin like the ones the dead high school kids had. She goes to Mulder's room, panicked about what they could be, but they turn out to be mosquito bites, so everything is okay again. Mulder and Scully talk for a while and Mulder tells where his interset in the paranormal and especially alien abduction stems from. He tells her the story if how his sister was abducted when he was 12 and she was 9, but he didn't remember until he under went hypnosis some years later.
      Mulder and Scully receive news of Peggy O'Dell being killed on the highway. Apparently she was walking, which is strange since she is wheelchair bound. The two agents find out that the coroners bay was broken into and vandalised. Mulder and Scully then return to their motel rooms, only to find they are on fire. Mulder is, understandably upset and throws his badge on the ground in frustration. He knows the fire was started to destroy the evidence he and Scully gathered during the case. Scully is pissed cause her laptop was in there with her field report of the case so far on it.
      The agents then meet with the coroner who did the post-mortems daughter, Theresa Nemman. She tells them how a bright light appeared when she was hangin out with her friends Billy Miles and Peggy O'Dell. She also tells them she has the same red marks as the others.
      Mulder tells Scully he thinks that Billy Miles is behind the whole thing and that he killed Peggy O'Dell. They then head back to the forest to search for more evidence. Scully finds a weird powder on the ground. She and Mulder are then told to leave as they are trespassing by Detective Miles. He and Mulder then see Billy carry Theresa Nemman to the same spot they other bodies were found. He is walking to everyones amazement. He and Theresa are then surrounded by a bright white light and a wind starts to get up, swirling around them. The light becomes blinding and then Billy and Theresa are left, with Theresa lying on the ground. The marks having mysteriously disappeared from Billy's body.
      Back in Washington DC, Scully is reporting to Blevins about the case and she gives him the piece of metal from the urangutan, which she had kept in her pocket and hadn't been destroyed in the fire. We then see Cancer Man in a room with long rows of shelves. He puts the implant in a glass case along with several others.