Super Soldiers
6 episodes of The X-Files carry this thread, 6h in all — 6 of them are in The Essentials.
In airing order

Mulder's request for reassignment to the X-Files is denied by Kersh, who hopes that Mulder will simply quit the FBI. When a census worker is killed on the White House lawn trying to get information to the President, Mulder gets in over his head trying to discover what the man knew.

After Agent Mulder goes beyond his jurisdiction to shine light on a possible X-file, Doggett is assigned to investigate the mysterious disappearance of two men aboard an oil rig. Once he arrives, he finds Mulder has taken it upon himself to start his own investigation. Mulder soon becomes convinced that the rig is drilling the black oil. Doggett and Mulder must attempt to stop the spread of the alien virus while avoiding the infected crew.

Agent Doggett investigates the death of an EPA official after his car is forced off a bridge by a woman he picked up. He asks for assistance on the case from Scully, who has returned to her teaching position at the FBI Academy in Quantico.

Doggett catches up with Shannon McMahon, the woman who the EPA official picked up. She claims to be a super solider and that the people she has killed were preparing the water supply and she wants Doggett to expose the truth.

When pieces of the spaceship beached in Africa resurface, the conspiracy within the FBI attempts to hide the information from the X-Files, especially the one person for whom the pieces have a special significance - Scully. When Doggett and Reyes discover that Scully and her child have been put in great danger, they race to protect her and William from the evil forces pursuing him, and Scully is forced to take drastic measures to protect her child.

Scully is anxious to recover William from his kidnappers and takes matters into her own hands when the FBI's attempts to assist in the investigation are less than helpful. With the help of the Lone Gunmen, Scully discovers terrifying information about her child's captors, and is once again forced to confront the mystery regarding the sinister interest in her son.