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The Cyber Ninjas are originated from a program called Cyber Initiative which is initiated by the Lin Kuei clan of assassins with the intention of transforming their warriors into cyborgs. It was campaigned by the Lin Kuei Grandmaster, who made an aggressive plan on turning many of the clan warriors: willingly or unwillingly makes no difference. Those that supported the Initiative felt that it would remove insubordination from their ranks, whilst those that opposed it believed that they were surrendering their free will.
The Grandmaster proceeded with his plans of transforming his warriors into cyborgs. Among those chosen were both Cyrax and Sektor; the former of whom had great reservations on this plan as he felt that it turned them into cold, soulless machines instead of true warriors.
Between post-MKII and pre-MK3, Smoke and Kuai Liang opposed to this initiative and fled the clan. They were relentlessly pursued, with Sub-Zero managed to escape but Smoke was not so fortunate. The three of them (Sektor, Cyrax and Smoke) were sent to eliminate Sub-Zero, but the cryomancer who is one of Raiden's chosen warriors, helped Smoke to regain his soul inside his mechanical body, so he joined Sub-Zero to fight Cyrax and Sektor, being successful. After that, however, Smoke was captured by Shao Kahn's forces, and was locked away in the bowels of Shao Kahn's Fortress in Outworld. Although Smoke regained his humanity he had to spend rest of his life in mechanical body.
Sektor fled, but Cyrax was also reprogrammed by Sub-Zero to destroy Shao Kahn. However, the emperor of Outworld was defeated before Cyrax could complete this task. Cyrax awaited for new orders but they never came. So he malfunctioned and wandered until becoming mired in the middle of Jade's Desert. Cyrax was eventually recovered and repaired by remnants of Lin Kuei. However, he appeared somehow different than when first constructed. Once again the clan sent Cyrax into battle, with his fellow cyborg Sektor assigned to monitor him.
After the defeat of the fallen Elder God Shinnok, it became apparent that Cyrax had begun to experience flashbacks of his former life. Special Forces agents Sonya Blade and Jax Briggs brought him to the Outerworld Investigation Agency (OWIA) headquarters, and used its technology to restore his humanity. Grateful for their help, Cyrax joined the OWIA as a scout in the realm of Outworld.
Many events would leave Sektor as the only active cyborg remaining of the three created, but during his many violent battles against Outworld forces, Sektor's program became even further corrupted: He believed the Lin Kuei Grandmaster to be inferior, and set his new objective to eliminate him and took control of the clan. Sektor successfully slew the Grandmaster, but was stopped from claiming the Dragon Medallion, the proof of the clan's leadership, by a returning Sub-Zero. Sub-Zero defeated Sektor in battle and claimed the title of Grandmaster. After his defeat, Sektor fled to Japan and formed the Tekunin, his own clan of cyborg ninja warriors to prove that Cyber Ninjas are superior to human counterparts.
With the death of the Grandmaster of the Lin Kuei and Sub-Zero assuming the leadership of the reformed Lin Kuei, the Cyber Initiative came to an end. Sektor, Cyrax, Smoke and Tekunin are perished at the final battle of Armageddon.
Following the death of the first Sub-Zero (Bi-Han. Who would later become Noob Saibot) at the hands of Scorpion in the Mortal Kombat tournament on Shang Tsung's Island, Raiden confronted Cyrax over the matter of the Cyber Initiative. The conflicted Lin Kuei warrior confessed to be one of those that spoke out against the Grandmaster's cybernetic conception, but ultimately decided that he served the leader of the Lin Kuei, regardless of the decision. However, after being betrayed by Shang Tsung, he openly opposed the Cyber Initiative and defeated Sektor, where he told his comrade to inform the Grandmaster that he was leaving.
Despite this being the case, both Sektor and Cyrax were converted into Cybernetic ninjas. Afterwards, they attempted to abduct Smoke to convert him as part of the Cyber ninja, but failed due to the intervention of Raiden. Instead, the second Sub-Zero was ambushed and successfully kidnapped, where he was transformed into a cyborg called Cyber Sub-Zero until the Earthrealm warriors managed to successfully restore his personality during Shao Kahn's invasion of Earth.
Sektor would assume leadership of the Lin Kuei and completely covert all members into cyber ninjas, killing anyone who refused to join his cause. With an enslaved Cyrax serving as his second-in-command, Sektor would set up a cloning program to create a vast army of cyborg ninjas devoted to serving him, replacing the need for slaving protocols within the converted. After training with Bo' Rai Cho and coming to terms with crimes he committed as Quan Chi's wraith, Sub-Zero attacked Sektor's secret headquarter and installed a virus that removed the slaving protocols, freeing Cyrax from Sektor's control. Sub-Zero would kill Sektor in single combat and take his head. While the remaining cyborgs installed Cyrax as their new leader, Cyrax instead chose to activate his self-destruct and destroy himself and all other cyborgs, asking Sub-Zero to rebuild their disgraced clan.
While Sub-Zero succeeded in restoring the Lin Kuei, a mysterious single surviving cyborg ninja, named Tri-Borg, would seem to be the last of the Cyber Initiative.
The Cyber Initiative would reform in the new timeline created by Kronika, where she appoints Frost the new leader and has her heavily cyberized after she was alienated by her former master Sub-Zero, who she deemed unfit to lead the Lin Kuei after Sub-Zero's allegiance with Scorpion, the grandmaster of their rival clan.
- Sektor (both timelines)
- Cyrax (both timelines)
- Smoke (original timeline)
- Cyber Sub-Zero (alternate timeline)
- Triborg (alternate timeline and DLC)
- Tekunin (both timelines)
- Frost (alternate timeline)
- Unit 5 (presumed to be in both timelines): Unit 5 is a minor villain in the Mortal Kombat video games series. He appears only in the 9th sequel. Unit 5 is a cyborg who worked for the Lin Kuei. He was given the assignment to locate Reptile. Eventually, he found his target and notified the Lin Kuei. This prompted Reptile to hide by cloaking his body. His invisibility was detected by Unit 5's sensors. The cyborg and the Saurian engaged in kombat. Unit 5 was immune to physical damage. Reptile killed him by spraying acid on his body. He took the cyborg's armor and left. Sektor and Cyrax arrived but Reptile was already gone.
- When Reptile wears a stolen cybernetic armor, he almost looks similar to Cyber Sub-Zero. His green appearance is the only exception.