Ep 2. Paper Clip (3)

Mulder and Scully's investigation of a secret government experiment that involves alien-human hybrids leads them to the discovery of a vast conspiracy involving the highest levels of the government and military. The episode begins with Mulder having a nightmare about the memory of Samantha's disappearance. He wakes up and notices that his gun is missing, and Scully comes in to check on him. Meanwhile, an old man named Albert Hosteen is killed while trying to access a secure military facility that is known to be connected to UFO sightings.

Mulder and Scully find evidence that leads them to believe that Hosteen was trying to retrieve records that could reveal the truth about the government's involvement in creating hybrid beings. They learn from a source that the government has been working on creating perfect alien-human hybrids, and that there is a secret project called "Nightwatch" that is key to their plans. The source is killed before they can get more information, but they manage to retrieve some documents that indicate that Nightwatch is a top-secret program that is above the level of presidential clearance.

Mulder and Scully meet with a man who claims to have been involved in the creation of the hybrids, and he tells them that Hosteen was seeking records that would compromise the entire project. He reveals that there is a secret cache of files hidden at an abandoned missile silo that could expose everything, but that they are guarded by military personnel who would kill to protect them.

Mulder and Scully team up with a group of activists who are working to expose the government's involvement in creating hybrids, and they all infiltrate the missile silo. They are able to locate the files, but they are ambushed by the military, and a firefight erupts. During the chaos, Mulder becomes separated from Scully and is forced to fight his way to safety.

The episode's climax sees Mulder discovering the truth about Samantha's disappearance and realizing that his father was a key figure in the conspiracy. The government cover-up goes all the way to the top, and Mulder has to outrun the military's pursuit in order to expose the evidence he has found and blow the cover on the conspiracy.

In the end, Scully and Mulder are left to contemplate the vast implications of their discovery, and the extent to which they have been manipulated by powerful forces. The episode serves as a pivotal moment in the series, as it sets the stage for much of the later episodes' exploration of the deepening conspiracy that threatens to engulf Mulder and Scully in its web.