For reasons unknown, he carried within him alien DNA and was capable of reading others' minds. During this time, he was targeted by the Syndicate because of his ability. After an assassination attempt on Praise failed, the Syndicate sent the Cigarette Smoking Man to kidnap him. While guarding Praise, Diana Fowley was intentionally shot and the Cigarette Smoking Man took Praise away. He was then seen getting into a car with the Well-Manicured Man and Alex Krycek. (TXF: The End)
Following the abduction of Mulder in 2000, John Doggett was made head of the FBI task force charged with his recovery. However, Doggett and Alvin Kersh were dead set against the possibility of there being alien involvement despite the objections of Scully and Walter Skinner. With help from the Lone Gunmen, they were able to deduce a pattern of alien appearances in the days after Mulder's disappearance and realized that the evidence suggested that Mulder was collecting the evidence for some reason. Scully suddenly remembered Gibson Praise, the only person who could provide definitive proof of the existence of aliens.Scully and Skinner traveled to Arizona, where the alien appearances had occurred, and were able to locate Praise at a school for the deaf. However, Doggett had been provided a file on Praise that was stolen from Mulder's office and arrived at the school alongside Scully and Skinner. Praise realized he was being sought and fled, only to be grabbed by Mulder himself and hauled away (TXF: Within).
Doggett tried to stop Mulder, who let Praise go free before walking backwards over a cliff and falling. However, Mulder's body was not found and Scully realized that they were not dealing with Mulder at all: it was actually the alien bounty hunter who was collecting evidence. Praise fled to an underground shelter where he and his friend Thea Sprecher sometimes went to hide. Scully followed Sprecher and found Praise with a broken leg. Scully returned to the school where Doggett and the FBI agents were still convened. She and Skinner returned to Praise, who said he could hear Mulder's thoughts and that was near. Unknown to any of them, Mulder was indeed nearby inside a spacecraft that was cloaked. Skinner drove Praise to a local hospital for emergency care to mend his broken leg.
The bounty hunter was not to be deterred, though. In the guise of Thea Sprecher, he entered the hospital, knocked out Skinner and made off with Praise. He was then rescued by Agent Scully, who killed the bounty hunter (TXF: Without).
It is revealed that Mulder spent a year living with Gibson Praise in Arizona after he left Washington D.C. while on the run from supersoldiers and the New Syndicate. Gibson Praise returned to testify on Mulder's behalf when Mulder was on trial for his life. Mulder first denied Gibson's appearance in the court room due to the fact that his supernatural powers might put him in danger. During the trial, Praise identified the Toothpick Man as a supersoldier, causing a small riot between Mulder and the court officials. After the trial, Gibson's whereabouts became unknown, though it is assumed that he was sent to safety by the government (TXF: The Truth).