On September 30, 1993, the Romanian Augment Vasily Hunyadi, the instigator of the civil wars consuming Yugoslavia in the early 1990s, lured Khan to the Ajorra caves in Central India. Once Khan and Joaquin were in position, Hunyadi triggered an underwater explosive charge with resulted in the earthquake in the previously considered aseismatic region of Maharashtra. Joaquin was gravely injured in the subsequent cave-in, receiving wounds from which a non-genetically engineered human would have surely died. Despite his enhanced status, he did not fully recover until April 1994.
In revenge for Joaquin's injuries as well as the deaths of the 10,000 Indian nationals who were killed in the earthquake, Khan enlisted the help of the American Augment Randall "Hawkeye" Morrison to do away with Hunyadi once and for all. On August 29, 1994, while Hunyadi was addressing the United Nations, the nerve toxin sarin gas, which was supplied by Morrison, was released in the Palais des Nations in Geneva, Switzerland. Within minutes, the gas had killed not only Hunyadi but many ambassadors and tourists as well, including Clare Raymond. (TOS novel: The Rise and Fall of Khan Noonien Singh, Volume 2)
He was one of 85 Augments who were placed in suspended animation aboard the SS Botany Bay by Gary Seven when the ship was launched from Earth on January 11, 1996. On Stardate 3141.9 in 2267, after 271 years drifting through space, the USS Enterprise discovered the Botany Bay. Joaquin was revived by Khan shortly thereafter and he assisted his master in his unsuccessful attempt to gain control of the Enterprise. Along with the rest of the surviving Augments, Joaquin was exiled to Ceti Alpha V at the order of Captain James T. Kirk. (TOS novel: The Rise and Fall of Khan Noonien Singh, Volume 2; TOS episode: "Space Seed")
Six months into their exile, in late 2267, Joaquin married Suzette Ling, Khan's chief of security, and they had a son named Joachim in 2269. He continued to serve as Khan's bodyguard as he had done in the 1990s. As Khan and his wife Marla McGivers were unable to have children, he began to groom Joachim from a young age to be his successor.
As was the case with many of Khan's followers, Joaquin was initially distrustful of Marla given that she had prevented Khan from killing Captain Kirk and had even assisted him in retaking the Enterprise from the Augments. While the Augments' suspicion of Marla lessened after she defied Khan and came to the defence of Zuleika Walker who had been accused of attempting to kill her, they never became friends. In spite of this, Marla was certain that they had one thing in common: they would both do anything to save Khan. After being implanted with a Ceti eel by Harulf Ericcson, the leader of the dissident Augments who ordered her to kill her husband, in 2273, Marla instead committed suicide in order to save Khan's life. Her self-sacrifice won her Joaquin's unqualified respect.
In 2279, both Joaquin and his wife Ling were killed in battle with the dissident Augments, who had seized Azar Gorge, the primary source of water for Khan's followers after the destruction of Ceti Alpha VI. Following his parents' deaths and because of their faithful service to him on both Earth and Ceti Alpha V, Khan raised Joachim as if he were his own son. (TOS novel: To Reign in Hell: The Exile of Khan Noonien Singh; TOS comic: "Khan: Ruling in Hell")
In an alternate timeline in which Khan won the Eugenics Wars and Humanity underwent genetic engineering en masse, Joaquin killed an unarmed man with a single movement of his sword following the conquest of New York City in 2012. By 2376, his direct descendants included Princeps Julian Bashir and Doctor Constantin Amoros, both of whom served aboard the Earthfleet vessel Defiance. (DS9 - Myriad Universes novel: Seeds of Dissent)