Malik was a Human augment, the product of 20th century genetic engineering, who was brought to life by Arik Soong in 2134. He was considered to be the strongest and smartest of Soong's augments, and was also the most ruthless.
Malik and eighteen other augments were raised by Soong on planet Trialas IV. As children, Malik and his "brothers" and "sisters" participated in classroom-like lectures taught by Soong, whom Malik and the others called "father". When Soong was captured and incarcerated in 2144 for stealing the augment embryos ten years earlier, Malik and the others were left to survive on their own, under the leadership of Raakin. Malik became attracted to Persis, but she chose to become Raakin's consort, believing him to be the strongest. Despite this, Persis fell in love with Malik, as well. (ENT: "Borderland", "Cold Station 12")
By 2154, Malik had grown tired of hiding on Trialas. That year, he and his "brother", Saul, captured a Klingon Bird-of-Prey, killing its crew in the process. The Klingons responded by threatening war with Earth over the incident. The Enterprise NX-01 was sent to capture Malik and the augments in order to prevent further confrontation.
Although Malik succeeded in acquiring a ship to escape Trialas, Raakin was enraged as he did not sanction the attack against the Klingons. Raakin knew that the Klingon Empire would be hunting for the augments, but Malik assured him that they would not find them. Raakin then ordered the Bird-of-Prey to another star system where the augments could live out their lives in peace. Believing Raakin had gone against Soong's wishes, Malik persuaded Persis to assist him in overthrowing Raakin as leader. With Raakin trapped by Malik and his followers, Malik killed Raakin, claiming it to be an "act of mercy". He then took command of the Bird-of-Prey and took Persis as his consort. (ENT: "Borderland")
Having received a signal from Soong, who was being held in the brig aboard Enterprise, Malik had the Brid-of-Prey dock with the Starfleet ship. As Malik spoke with the ship's captain, Jonathan Archer, Persis led a group of augments to free Soong. Malik himself took Archer as a hostage to ensure he returned to the docking bay without incident. Upon arriving at the bay, he released Archer and was reunited with his "father". Soong and the Augments then boarded the Bird-of-Prey and, leaving behind a disabled Enterprise, set a course for Cold Station 12 to retrieve the remaining 1,800 augment embryos still in cold storage. (ENT: "Borderland", "Cold Station 12")
On Cold Station 12, station director Jeremy Lucas refused to give Soong the code which would open the stasis chamber containing the embryos despite a painful interrogation. Malik suggested they torture one of Lucas's colleagues to get the director to talk, an option Soong reluctantly accepted. Malik tortured the station's deputy director by infecting him with one of the station's many stored pathogens, Symbalene blood burn. When Lucas still refused to give up the code, Soong, unwilling to see anyone die, ordered Malik to release the anti-pathogen. But Malik refused, forcing Soong to take over the station's controls, but by the time he was able to release the anti-pathogen, the deputy director had died.
When Archer, Phlox, and other crewmembers were captured while attempting to infiltrate the station, Malik learned that Lucas and Phlox were friends and, again defying Soong's orders, he placed the Denobulan in the pathogen booth. Before releasing the pathogen, however, Lucas opted to input the code for the stasis chamber. As Soong collected the embryos, Malik stole several containers of infectious diseases without Soong's knowledge. He planned to use these infection diseases as a bioweapon to destroy a nearby Klingon colony, thereby pitting Starfleet against the Klingon Empire.
Before leaving, Archer made one final attempt at gaining control of the situation, but Malik was able to defeat him, although he remarked that Archer was a "competent fighter". Believing the attack to be a reasonable excuse to justify Archer's murder, Malik set every stasis field in the station to collapse, which would have released the hundreds of fatal pathogens stored there. After Malik left, however, Archer and the others were able to escape the pathogens. (ENT: "Cold Station 12", "The Augments")
When Soong learned of Malik's plan to destroy a Klingon colony and refused to allow it, Malik reclaimed command of the augments and imprisoned Soong in his quarters. Although she sided with Malik in imprisoning Soong for fear Malik would kill her, Persis later helped Soong escape. However, Malik knew Persis was responsible, and killed her. As she died, he proclaimed he would miss her, and stole her last breath with a kiss.
Malik was ultimately successful in launching the torpedo carrying the diseases, but it was destroyed by the Enterprise. Even though Malik disabled most of the Enterprise's weapons, the aft phase cannon was still functional. The Enterprise used it to disable the Bird-of-Prey. Refusing to be captured, Malik overloaded the dilithium matrix and destroyed the ship. However, he was able to transport himself to the Enterprise before the Bird-of-Prey was destroyed. On Enterprise, Malik attacked Soong with the intent of killing his "father" for betraying his children, but was himself killed by Archer with a puncturing particle rifle blast through the torso. (ENT: "The Augments")
The third issue and fifth issue of the comic Star Trek: Khan shows Malik as one of the alternate Khan's followers in 1996, and part of his crew on the Botany Bay. It is not explained how he would have been present in 1996 and on the Botany Bay.