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In July 1947, Carlson was called in to assist the United States government, who had recovered an alien vessel which had crashed near Roswell, along with its occupants Quark, Rom and Nog. The vessel, Quark's Treasure, had accidentally been sent back in time from 2372. Constable Odo was also on board, though he had disguised himself to catch Quark in the act of kemocite smuggling. Carlson and Garland did not agree with General Rex Denning and Captain James Wainwright's belief that the Ferengi represented the vanguard of an invading alien army. They instead believed that they were peaceful and harmless explorers who had much to teach humanity about the universe. When it became clear that Wainwright was planning to use any means necessary to extract information from the Ferengi, Carlson and his fiancée helped them to escape from Roswell. They later claimed that the Ferengi manipulated them into doing so, using their "insidious mind-control powers." (DS9 episode: "Little Green Men")
On September 23 of that year, Carlson recruited Wainwright into the newly created Majestic 12, a secret organisation whose mandate was to collect evidence of extraterrestial activity on Earth and develop strategies to combat potential alien invaders. Wainwright was surprised by the offer as he was under the impression that Carlson considered him "to be little more than a typical brainwashed military robot, incapable of exercising any thoughts not already programmed into him by his superiors." He was also suspicious of Carlson and Garland's claim to have been manipulated by the Ferengi into helping them escape. Carlson was aware of Wainwright's doubts about him but recruited him regardless. (TOS novel: From History's Shadow)
Carlson later married Faith and was employed at Area 51. In 1986, Project F (as Carlson's operation was known) had a burst of activity after Naval Intelligence gave them several devices recovered from an intruder captured aboard the aircraft carrier USS Enterprise while it was docked at Alameda Naval Base. However, before they conducted more than a cursory examination of the devices, a mysterious woman who somehow got past Groom Lake's intense security took the devices. (TOS novel: The Rise and Fall of Khan Noonien Singh, Volume 1)
By the 1990s, one of the top secret projects being worked on was the top secret DY-100 sleeper ship, with people such as Dr. Marcus Walter Nichols and pilot Shaun Geoffrey Christopher working on the project. Roberta Lincoln also provided technical assistance, giving Shannon O'Donnell access to technological specifications to help complete the ship. Once the unnamed ship was completed, Lincoln and O'Donnell launched the ship into orbit on January 5, 1996. As instructed, O'Donnell later claimed that she was under Ferengi mind control at the time when questioned about the incident. While no charges were brought up against her, O'Donnell did lose her position at the government lab. Off the record, Carlson told O'Donnell that his wife Faith, who had died prior to 1996, had been the one who came up with Ferengi mind control in the first place. (TOS novel: The Rise and Fall of Khan Noonien Singh, Volume 2)