The light turns out to be from a couple of divers coming down to the wreckage; Mulder tries to escape, but is captured and put under military arrest for interfering with military investigation into the plane crash. Pendrell's shooter gets away despite his wound, and Skinner informs Scully that the controller (Sgt. Louis Frish) is being put under military arrest on an order from the Joint Chiefs of Staff, due to suspicion of murder and providing false testimony. The military has concocted a cover story that a fighter jet accidentally collided with Flight 549.
Scully tells Mulder that the woman claiming to be Fenig's sister was actually an unemployed aeronautical engineer who met him in a mental institution. At Fenig's trailer, the agents find a recording of him declaring that he is devoting his life to finding proof of alien existence. At the lake, the military recovers the wreckage and alien bodies, and one man is seriously burned by radiation. Upon seeing this, the suspicious NTSB man declares, "We found it."
Mulder gives his theory: that Fenig was on board with an object proving alien existence, that a hitman was following him was trying to take it from him, and that Max was abducted by aliens mid-flight. Mulder believes everything would have been OK, and nine minutes would have been erased from everyone's memories, but instead the military shot down the UFO, leaving the plane's door open and leading to its crash. However, he feels the only way to prove it is if he finds the object Fenig was carrying. Unfortunately, his knapsack has been found but all it has is Fenig's NICAP hat.
Scully visits Fenig's not-sister, now re-committed, and she tells Scully that she stole a three-section alien power source from a military employer and divided it up. She and Fenig each had a piece, both apparently recovered by aliens during abductions. Back at Fenig's trailer, Mulder discovers a letter from a DC address with a luggage claim ticket. He recovers the third piece at an airport, and boards a flight back to the capital.
The NTSB man is also on board, but Mulder realizes who he is and imprisons him in the lavatory, vowing to bring him to justice and expose the artifact. Mulder sees his watch stop and tries to get a stewardess to have the captain do evasive maneuvers, but to no avail. The NTSB man gets free, takes the package, and ends up getting abducted; Mulder is left artifact-less and missing nine minutes. Fenig's not-sister takes over his work and the "Max Fenig Rolling Multimedia Library and Archive." The episode ends with Scully musing over Mulder's gift from the first part, and how advances are made through perseverance and cooperation and sacrifices must not be forgotten.
Episode Body Count
Agent Pendrell: dies after being shot in the lung by the NTSB man.
At least five more aliens: seen in body bags at the military's recovery operation.
Cumulative Body Count (91/202 episodes, 0/2 movies)
Humans: 1,180Creatures: 80
Grand Total: 1,315
Note: "Tempus Fugit" and overall count updated after a friend suggested that the surviving passenger probably didn't make it.