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Throughout most of his career in Starfleet, Halloway served at the Utopia Planitia Fleet Yards, Mars, as an engineer, designer and supervisor. Throughout the 2350s and early 2360s, Halloway oversaw the construction of the Galaxy-class USS Enterprise-D at the Yards, along with Commander Orfil Quinteros, who became a good friend.
As the construction of the Enterprise was completed, Admiral Norah Satie and Starfleet Command decided that Halloway should be the Enterprise commanding officer on its long-term voyage of exploration. Halloway initially accepted the honor, but his wife, Solveig, wasn't set on a life in space, as her chosen career would be of little or no use aboard a starship. Additionally, a number of accidental deaths during the Enterprise construction left him unsure whether command was for him.
Following the Enterprise commissioning ceremony in late 2363, Halloway informed Satie he would turn down command. In his place, Satie assigned Captain Jean-Luc Picard as Enterprise CO. Around this same time, he and his wife purchased a home on Luna.
Halloway remained at Utopia Planitia, where he worked first on the design of the Andromeda-class explorers, and then supervised construction of the Nebula-class USS Melbourne. This ship was five weeks from flight in early 2367 when the Borg, led by Locutus, threatened Earth, and an armada was called to Wolf 359. Halloway took command of the still-incomplete Melbourne in that battle, and was killed in action.
Although Halloway never met Jean-Luc Picard, he left a message for him which spoke of the decision that he made, and how he couldn't leave his family. (TNG short story: "Meet with Triumph and Disaster", "Trust Yourself When All Men Doubt You")
In an alternate timeline experienced by Captain Jean-Luc Picard in 2369, Thomas Halloway was the commanding officer of the USS Enterprise-D, while Picard was a junior science officer. (TNG episode: "Tapestry")