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Ambrose Chapel is a Central Intelligence Agency (C.I.A.) Agent. He was impersonated by the alien bounty hunter.
We first meet Chapel when he approaches Mulder at Scully's apartment complex. There he tells Mulder that he needs to talk to him about a case. Chapel tells Mulder, "I have a story to tell Agent Mulder. Believe me, you'll wan to hear it."
Inside Scully's apartment, Mulder and Scully listen to Chapel tell about a Russian Science Program called, Gregor. He tells Mulder and Scully that the Gregors main purpose is to "destroy the country's immune system." He further tells Mulder and Scully that these Gregors are now being "systematically eliminated" by a Russian spy killer, in exchange for the absolute suppression of the program's existence and to obtain the science that created it.
When Mulder asks Chapel, "What's your business in this?" Chapel replies by telling Mulder that they share a similar sentiment in their government's policies of denial. Furthermore, Chapel tells Mulder that the Gregors have been trying to contact Mulder. Chapel tells Mulder and Scully that he knows they've been inquiring about the recent Gregor deaths. Chapel pulls out the newspaper clipping with the picture of Dr. Landon Prince and admits to placing the ad.
Mulder tells Chapel they have located Dr. James Dickens, one of the Gregors.
In the next scene, we see Mulder, Scully, and Ambrose waiting in a car, outside Dr. Dickens apartment complex. When Dr. Dickens and his female assistant arrive at the apartment, Mulder, Scully, and Chapel proceed up to Dr. Dickens apartment unit. When they knock at the door, they are greeted by Dr. Dickens. We see that Dickens instantly recognizes Chapel. Dickens turns around, runs and jumps out the window. He survives the fall and runs into the dark street. Mulder and Chapel take chase.
Eventually, Dr. Dickens ends up in an alley with no way out. As he looks around for another way out, he sees Chapel coming down the alley. Dickens tries to climb up via an fire escape ladder but his leg is grabbed by the alien bounty hunter. In the next scene we see Scully with a gun drawn, walking down the same alley where Dickens was trying to escape. Chapel appears from behind a trash bin and tells Scully that Dickens got away via the escape ladder.
Back at Mulder's office, Scully voices her doubts about Chapel's story and involvement in the case. She questions Mulder's trust in Chapel. Mulder defends Chapel's trustworthiness by citing his service as a 17 year veteran, special intelligence clearance, and assuring Scully, "he's the real thing."
Scully then points out that a man with Chapel's experience wouldn't need their help or wouldn't allow Dr. Dickens to easily escape. Scully tells Mulder of her observation that Dickens wasn't running away from them but from Chapel.
As Mulder is called off to a personal family matter, Scully heads off to Germantown, Maryland in search of Dr. Dickens. At Dr. Dickens medical facility, Scully finds Chapel tipping over several glass canisters filled with green fluid and on the floor are what look like formed organic tissues. Chapel steps on one of these, causing it to ooze green jelly.
Scully quielty leaves, but Chapel suspects someone is watching him. He heads out the door in time to see Scully quickly driving away in her car.
Mulder learns from his sister that Chapel is the bounty hunter killing the Gregors and soon will come after her. Mulder calls Scully to warn her but is unable to talk to her and instead leaves a voicemail to not trust the C.I.A. agent. Samantha tells Mulder that the bounty hunter can disguise himself as anyone. This is the last time we hear of Ambrose Chapel. (TXF: "Colony")
The name "Ambrose Chapel" is a key plot point in the Alfred Hitchcock film The Man Who Knew Too Much (1956).