In the mid-24th century, Leyton was captain of the USS Okinawa, with Benjamin Sisko as executive officer. The two generally had a good working relationship. Leyton was a decisive captain, but appreciated Sisko's honesty.
Leyton and his crew served in the Federation-Tzenkethi War. It was during this conflict that the Okinawa encountered three Tzenkethi raiders, which Leyton decided to pursue into an asteroid belt. During a staff meeting, Sisko voiced his opinion that chasing the raiders was an "unnecessary risk," and continued to press his point in the ready room even after Leyton had made his decision. Leyton responded that "a good officer has to respect the chain of command. There comes a time when you have to accept the orders of a superior officer and carry out his orders, whether you agree with them or not." Sisko later conceded that Leyton's decision was the right one.
In 2371, Constable Odo, the Changeling chief of security on Deep Space 9, learned from one of his people that Changelings had infiltrated the Federation. Not long after Odo gave this information to Starfleet, Leyton, by now an admiral, led a contingent of high-ranking officers to meet with Federation President Jaresh-Inyo to recommend implementation of sweeping security measures meant to protect Earth, measures which Jaresh-Inyo rejected as "extreme." (DS9: "The Adversary", "Paradise Lost")
The next year, when the Dominion bombed a high-level diplomatic conference between the Federation and the Romulan Empire taking place on Earth, Leyton became convinced that the Changelings posed a greater threat to Earth than the president was prepared to deal with, and initiated a conspiracy to attempt a military takeover of Earth. Assigning Sisko, by this time a captain, as acting head of Starfleet Security, Leyton utilized an elite group of Starfleet cadets known as "Red Squad" to sabotage Earth's global power grid in an attempt to spread paranoia regarding Changeling infiltration. When Sisko uncovered Leyton's plot, he ordered the USS Defiant to bring Lieutenant Arriaga, a conspirator stationed at Deep Space 9, to Earth, where he could testify that Leyton ordered him to attach a subspace modulator to the relay satellite at the far end of the Bajoran wormhole, which caused it to open and close at random, making it appear as if a cloaked Dominion fleet was entering Federation space. Leyton subsequently had Sisko framed as a Changeling infiltrator and imprisoned, but Odo was able to break Sisko out.
Leyton ordered Captain Erika Benteen, commander of the USS Lakota, to intercept the Defiant and prevent them from reaching Earth, telling her that the entire crew had been replaced by Changelings. Sisko, however, was able to convince Benteen that Leyton had been lying to her, and she called off her attack, allowing the Defiant to reach Earth. When it became clear that his plot had failed, Leyton offered his resignation. (DS9: "Homefront", "Paradise Lost")
Background information Edit
The script for "Homefront" describes Leyton as, "in his mid-fifties, tall, healthy and looks younger than he is. He's a veteran of conflicts with the Romulans, Tholians, Cardassians and Borg." It also says he held the position of Head of Starfleet Operations, though this was never confirmed in dialogue. (Star Trek: Deep Space Nine Companion - A Series Guide and Script Library), 
Foxworth played a similar role of General Hague on the series Babylon 5. On that show, his character also attempted a military takeover of Earth, but the attempted coup was shown in a very different light, as an attempt to overthrow a totalitarian government. Foxworth was originally set to reprise his role in the episode "Severed Dreams", but was unable to do so, as he was filming Star Trek: Deep Space Nine at the time. As such, his character was killed off-screen, and the role changed to that of Major Ryan, played by Bruce McGill. In an outtake for the episode, when asked where General Hague was, McGill jokingly answered, "General Hague is doing Deep Space Nine. It seems he was double-booked by his agent, there was nothing to be done." 
Leyton appears in the Star Trek: The Lost Era novel Catalyst of Sorrows, which confirms he held the position of Chief of Starfleet Operations in 2372. It also states Leyton was the one to promote Sisko to the rank of lieutenant commander and first officer on the Okinawa. He also features in the Star Trek: Typhon Pact novel Rough Beasts of Empire in scenes set during the Tzenkethi War in the 2360s.
There were also plans for a Lost Era novel that would have involved Leyton and Sisko on the USS Okinawa during the Tzenkethi War, but due to the firing of Marco Palmieri and other Star Trek writers at Pocket Books, the story never developed past the planning stage.  
The Pocket DS9 novel Hollow Men reveals that Leyton was sentenced to five years imprisonment in the New Zealand Penal Settlement for his crimes. In 2374, he receives a visit from Benjamin Sisko following the events of "In the Pale Moonlight", in which Sisko tricks the Romulan Empire to join the war against the Dominion.
In the novel Articles of the Federation, Leyton's manipulation of Jaresh-Inyo into declaring martial law later proves to be a deciding factor in 2372's presidential election. President Jaresh-Inyo is defeated after only one term by Federation Councilor Min Zife of Bolarus, who favors a more militant stance against the Dominion in preparation for the coming war.
Leyton further appears in the Star Trek: Myriad Universes novel A Gutted World, which is set in an alternate timeline in which the Cardassians never leave Bajor and the Bajoran wormhole is never discovered. In the book, Leyton serves as commander of the fleet that defended Earth from the Borg at the Battle of Sector 001 and is later killed in action.
The novel Hollow Men calls him James Leyton, while the novel The Poisoned Chalice calls him Robert Leyton. The Decipher RPG module Starships calls him Thomas Leyton. The Autobiography of Jean-Luc Picard calls him Rodney Leyton.
Leyton is also mentioned, though does not appear, in the Star Trek Online novelization The Needs of the Many, when Jake Sisko's talks of a traitor from the recent Undine War and people committing treason in the name of saving the Federation.