In 2372 General Martok commanded the empire's defense forces during a massive invasion on Cardassia, brought about by suspicions that the Cardassian Detapa Council was under the control of Dominion shapeshifters. Martok led the attack from his flagship, the Negh'Var, but his mission was thwarted when the Cardassian council was rescued by Captain Sisko of Deep Space 9. Martok subsequently turned his attack onto the Federation-controlled station, but Gowron decided to end the battle and return home over Martok's objections.
It was not realized that sometime before 2373, Martok was captured by the Dominion while hunting sabre bear on Kang's Summit and replaced by a Shapeshifter. The imposter wielded influence upon Gowron, urging him to war with the Federation over the Archanis IV dispute, but was also poised to take over when the Founders tried to bring about the assassination of Gowron. However, the imposter was exposed and killed at Ty'Gokor. Meanwhile, the real Martok was being held by the Jem'Hadar at Dominion Internment Camp 371 in the Gamma Quadrant, where he was forced to fight Jem'Hadar in hand-to-hand combat, which caused the loss of his left eye. He escaped in 2373 along with Worf, Dr. Bashir and Garak, and returning to the Alpha Quadrant, he was made commander of the Klingon forces on Deep Space 9.
Later that year Martok assumed command of the bird-of-prey Rotarran under orders to search for the missing battle cruiser I.K.S. B'Moth. He found himself with a crew demoralized by a series of punishing losses at the hands of the Jem'Hadar. Although they were badly in need of a victory, Martok proceeded cautiously, so much so that Worf believed he was paralyzed by fear of the Jem'Hadar and challenged him for control in a death match. Seeing Martok and the crew revitalized by the bloodlust on display, Worf let Martok win, and the ship subsequently defeated an enemy vessel and rescued the 35 survivors of the B'Moth. So grateful was Martok that he made the Worf a member of the House of Martok. Later he granted the same honor to Worf's son, Alexander Rozhenko.
Martok's wife was Sirella, who carried the title of Mistress of the House of Martok and therefore had to approve of Worf's bride, Jadzia Dax, before they could get married. Martok and Sirella had a number of children together.
Martok was a complex man. He was a shrewd judge of character and cared deeply about those under his command. Martok even appointed Worf as first officer on a dangerous mission to Monac IV in early 2375 so that Worf could earn entry into Sto-Vo-Kor for his Jadzia, who had recently died. But he could also be ruthless, having had Kaybok of the I.K.S. M'Char executed in 2372 for disobeying orders.
On Stardate 51247.5 Martok was promoted to supreme commander of the Ninth Fleet, stationed at Deep Space 9 to defend the strategically critical Bajor Sector against Dominion and Cardassian aggression. Martok commanded the Klingon wing of the allied Alpha Quadrant fleet that successfully captured the Chin'toka System from Dominion control in 2374. Martok's battlefield acumen was critical in several victories by the Alpha Quadrant powers. Unfortunately, the resulting accolades caused Chancellor Gowron to fear that Martok might soon become a political rival for leadership of the High Council.
In 2375 Gowron seized direct command of the Klingon military and ordered Martok to undertake a series of foolhardy combat engagements, resulting in terrible losses among Klingon forces. Martok was blamed for these costly defeats, but refused to question Gowron, even though he knew that Gowron had intended the missions to undermine Martok's image. It was Worf who challenged Gowron and subsequently killed him. By all rights Worf was entitled to assume leadership of the High Council, but he declined and instead handed the title of Chancellor to Martok.
Martok continued to command Klingon forces in the Allied invasion on Cardassia that resulted in the surrender of the Dominion. Seeing the devastation inflicted upon the Cardassian people in the war's aftermath, Martok's comrades Admiral Ross and Captain Sisko refused to partake in a victory toast of bloodwine, but Martok had no problem downing the drink by himself. He later collaborated with Admiral Ross to offer Worf the position of Federation Ambassador to Qo'noS. Worf accepted, which delighted Martok because now he had someone to go targ hunting with.