Scully undergoes hypnosis in a effort to remember what happened at the mass burning site.

In this continuation of the previous episode... a man, his face unseen, types a letter to his son (whose identity is unknown). The man, who lives in a remote cabin, addresses the letter to the FBI and pays a boy to mail it.

Meanwhile, rescue workers sift through the area near the dam where blackened bodies lie along the length of a bridge. Amongst the bodies is Quiet Willy, the Syndicate's hit man. Skinner directs Mulder to a nearby provisional tent, where Scully is ministered by medics. Nearby is the body of Dmitri, the Russian boy, his exposed skin blackened by the fire. When Scully regains consciousness, she tells Mulder she has no memory of what occurred at the dam. Outside of Scully's room, Spender tells Mulder that rescue workers were unable to locate his mother, Cassandra.

The Well-Manicured Man and a physician, Dr. Bronschweig, tend to Maria Covarrubias inside a hospital quarantine room. Later, the Well-Manicured Man speaks with Krycek, imprisoned aboard the Russian freighter. The Well-Manicured Man is aware that Krycek deliberately exposed Dmitri to the black oil to insure the infection of anyone who attempted to ascertain what he knows about the burnings in Russia. He also believes that Krycek possesses a vaccine, that would create resistance to the alien colonists. The Well-Manicured Man offers Krycek freedom in return for the vaccine.

Meanwhile, a spacecraft crashes at Fort Wiekamp Air Force Base. A faceless alien pirate drags one of his comrades from the wreckage. Later, members of the Syndicate study photographs of the alien. They realize the man is a resistance fighter, a member of an ongoing battle against alien colonists. The Well-Manicured Man explains that Krycek gave him the vaccine, meaning resistance may, in fact, be a possibility. But the Elder concludes that the captured fighter should be turned over to the colonists, the Well-Manicured Man has Covarrubias injected with the vaccine to ensure it actually works.

Back at the hospital, Mulder tells Scully that x-rays have revealed the presence of implants inside the people who were at the dam. Mulder recounts his belief that the U.S. government manufactured and implanted the chip as part of a bio-chemical weapons project. Scully agrees to be hypnotized by Dr. Werber in an effort to recall what happened at the dam. In a trance-like state, Scully recalls how a UFO flew overhead, and shortly thereafter, how the faceless aliens set congregants on fire. Then another craft appeared overhead, which began attacking the faceless men. Cassandra was then pulled upward, out of her wheelchair, by the ship. Afterward, Werber tells Mulder that the same event will happen yet again.

Skinner reviews an audio tape of Werber's session with Scully. Mulder tells Skinner the entire event was staged to cover up a classified military project. Skinner admits, however, that Scully's UFO scenario is more plausible. Meanwhile, when Covarrubias fails to respond to the vaccine, the Elder informs the Well-Manicured Man that the captured alien is being turned over to the colonists.

Spender shows the agents a videotape of himself, as a young boy, answering questions while under hypnosis. As the tape plays, the young Spender describes his abduction by a UFO. Spender then pauses the tape. He tells the agents the story is untrue, a falsehood told to him by his mother many times. He maintains that Dr. Werber's regression memory theory is without merit. Spender also points out that Mulder has expressed his UFO theories to Scully many times... suggesting that she has recounted the information in a similar manner.

Krycek surprised Mulder inside his apartment. He explains that Kazakhstan, Skyland Mountain and the site in Pennsylvania are all beacons for colonization. The burnings, Krycek explains, were the work of alien rebels attempting to foil the colonist's plans for takeover. Krycek gives Mulder the location of the captured alien rebel. He maintains that if the captive perishes, so does the resistance.

Accompanied by Scully, Mulder drives to Fort Wiekamp. As they attempt to bluff their way through the front gate, the agents notice Quiet Willy at the wheel of a military truck as it is about to exit the base. As the vehicle pulls away, Mulder sneaks aboard the cargo area. There he finds faceless alien pirate imprisoned inside. Quiet Willy brings the rig to a stop... then morphs into the alien bounty hunter. He climbs into the cargo area, but shortly thereafter, a white light illuminates the truck. A second faceless alien, armed with a firestarter weapon, enters. Mulder opens fire. Shortly thereafter, a confused Mulder is swarmed by MPs and placed inside a car with Scully. Mulder has no memory of how he got aboard the truck. Meanwhile, the envelope seen in the opening teaser is delivered to Spender. Several days later, back at the cabin, the envelope, labeled with the words "return to sender," is delivered to the Cigarette-Smoking Man.