In an episode with revelations referring back to the episode Fallen Angel, Mulder and Scully investigate the downing of a jetliner, apparantely by a UFO.

The episode starts as we witness the mysterious downing of a jetliner, Flight 549. The last thing Max Fenig who is sitting there sees is a tremendous wave of light open the airline door which is next to him. A short time later at 'The Headless Woman's pub', Mulder and Scully are approached by Sharon Graffia who tells the agents she is Max Fenig's sister (the UFO nut from Fallen Angel). She informs them that Max had just been killed in a plane crash and it was his wish that they be found.

Mulder and Scully travel to the crash site accompanied by Go-Team members where they listen to a radio transmission seconds before the crash happened. The pilots speak of an 'intercept' and Mulder believes this is the work of the UFO much to the humour of the rest of the team. He also finds that there is a 9 minute time difference between the time of the crash and the time on the passenger's watches while searching the crash site. Remember the last time the agents were missing nine minutes?

Meanwhile an investigator named Garrett is spraying bodies from the wreckage with some sort of acid which is dissolving their bodies and destroying the evidence. The agents find Fenig's body among the debris and later his sister's body is also found elsewhere having previously gone missing from her motel room. Mulder believes she was abducted by a UFO.

Back at the Headless Woman's pub, Scully is confronted by Garrett while she is with an army officer named Louis Frish whose life is in danger because he can prove that the military is responsible for the plane crash and the downing of the UFO. Garrett shoots Agent Pendrell (who happens to be at the bar) in the chest but Scully quickly responds by shooting him in the leg. After this incident, Mulder examines a map and finds out that a second craft must have crashed into a lake called Great Sacandaga. He scuba dives into the lake where he uncovers a wreckage and the body of an alien. But suddenly a bright flash of light arises from the wreckage and we are left with the words 'To be continued' for another agonizing week.