In the realm of Outworld, Motaro's race of Centaurians had come into conflict with the Shokan. Shao Kahn, Emperor of Outworld, had begun to favor the Centaurians over the Shokan, and had been punishing the latter, aiding the Centaurians in the defeat and subjugation of the Shokan race. When Kahn formed special extermination squads to eliminate the chosen warriors of Earthrealm during his invasion, Motaro was appointed to head this elite group of savage warriors. He was the one who killed Johnny Cage in the events of MK3/UMK3/MKT.
Sonya Blade's defeat of Kano during the events of Mortal Kombat Trilogy had resulted in the Black Dragon member being thrown from a skyscraper to the streets below. Motaro recovered the severely injured Kano, and brought him back to Shao Kahn's fortress. After reviving him with magic, Motaro then imprisoned the criminal so that he could later be punished by Kahn for failing to defeat Sonya.
It is at this point that Motaro was assaulted and supposedly killed by Sheeva. However, he survived but barely as he returns in Mortal Kombat: Armageddon, but since then the Centaurs have been put under a curse by the Shokan, turning him and the rest of his race into bipedal Minotaurs. This gave him and his race another reason to hate the Shokan. Motaro swore to make the Shokan pay dearly for this act.
In Motaro's Armageddon ending, he defeats Blaze, causing the firespawn's essence to consume him. When the fire stops, Motaro finds himself walking on four legs again, having lifted the Shokan's curse on the Centaurs. He vowed that the Shokan would pay dearly for their treachery.
Ultimately, as with nearly every character of the franchise, Motaro is killed at the end of Armageddon. How or by whom is not known. In the alternate timeline, he assumes much of the same role as he did before, leading the extermination squads of Shao Kahn into Earthrealm. However, this time, he is killed by Raiden, who foresaw that Motaro would kill Johnny Cage. Mileena later brings Motaro's body back to Shao Kahn. Motaro is then replaced in command by Sindel.