While the original Lin Kuei was founded pre-Mortal Kombat, some time around the second tournament in Outworld, during the false tournament in the original timeline, the Lin Kuei Grandmaster felt his clan would be more effective if upgraded and augmented into cyborg assassins. Many of the most well known Lin Kuei assassins would eventually be converted, whether this being on purpose or against their will. The only known assassin to not be converted is Bi-Han, who was resurrected as Noob Saibot by the time the Cyber Initiative came to fruition. While most of the significant and well known Lin Kuei were converted, it is unknown who Triborg is, as he is the only more advanced cyborg assassin produced for the Cyber Lin Kuei due to his shapeshifting abilities.
The Grandmaster pushed for the Lin Kuei to become cyberized during the false Mortal Kombat Tournament that would be held in Outworld. Sektor was the only one to follow his father's wishes and was the most sucessful result of the Cyber Initative. Cyrax would soon follow suit while Sub-Zero and Smoke would flee the clan to avoid cyberization. Smoke was then captured while Sub-Zero managed to escape, resulting in Smoke to become cyberized. Sektor, Cyrax and Smoke were all tasked with hunting down and killing Sub-Zero, who was now deemed a traitor for abandoning the Lin Kuei. Sub-Zero would manage to reprogram Cyrax, who would later regain his soul's integrity and join the Special Forces while Smoke becomes deactivated in an Outworld prison. Smoke would be reactivated by Noob Saibot and forced to be his ally for some time before being freed from his control by Sub-Zero.
Sektor's programming would later be corrupted, with him viewing his father as an inferior Grandmaster to the Lin Kuei, resulting in Sektor killing him. A battle for the mantle of Grandmaster was ultimately won by Sub-Zero, leading Sektor to be the last of the Cyber Lin Kuei due to Cyrax and Smoke regaining their memories and humanities and Sub-Zero restoring the Lin Kuei. He would flee to Japan and establish a new cybernetic clan called the Tekunin, bringing an end to the Cyber Lin Kuei.
All three cyborgs, alongside Sub-Zero and many kombatants would perish in the Battle of Armageddon.
Many aspects of the original timeline are still present however specific changes occur.
During the tenth Mortal Kombat tournament, Cyrax is more hesitant about the Cyber Initiative when confronted by Raiden about it, revealing he is against it, however he still wishes to serve the Lin Kuei despite this. After refusing to complete Shang Tsung's task in killing Johnny Cage, Cyrax would leave the Lin Kuei after a confrontation with Sektor who believed the Cyber Initiative would remove these worries from Cyrax and perfect him. Later in the Living Forest, Smoke is confronted by a now cyborg Sektor and defeats him, but is ambushed by many Cyber Lin Kuei for capture and automation. Raiden would intervene in the attempted capture of Smoke, preventing him from becoming cyberized. In Shao Kahn's Arena where the second tournament is being held, the younger Sub-Zero wishes to confront and kill Scorpion for the murder of Bi-Han, and, after defeating the Spectre, he too is ambushed by the Cyber Lin Kuei by Sektor and a now cyberized Cyrax, much to Smoke's dismay and Raiden's regret. Shao Kahn allows them to take Sub-Zero and in return, the Cyber Lin Kuei would pledge their allegiance to the Outworld Emperor. The Cyber Lin Kuei continue to assist Shao Kahn during his invasion of Earthrealm, where a previously wounded Kabal encounter a now cyberized Sub-Zero. Kabal defeats him, where Raiden and Smoke take him back to a hidden location and reprogram him with Kabal's help, regaining his emotions and thoughts and rejoining Earthrealm's side in the war. Sektor is aware of his reprogramming and attempts to kill Sub-Zero but is defeated. He eventually encounters Noob Saibot and Quan Chi attempting to create a Soulnado for Shao Kahn, however Noob is defeated by his brother and Quan Chi is defeated by Nightwolf. Sektor and Cyrax would lead an ambush with the Cyber Lin Kuei against the Earthrealm defenders at their secret location but are defeated in the process. Sub-Zero, along with many of the Earthrealm defenders are killed by Sindel and later transformed into Revenants by Quan Chi. Sektor and Cyrax are not seen after the Cyber Lin Kuei attack.
Sub-Zero's body would be transformed back into a human body, but was still a Revenant serving Quan Chi during the Netherrealm invasion of Earthrealm. He would be revived and returned to his human form by Raiden, who also restored Scorpion and Jax Briggs. Sektor, now the Grandmaster of the Cyber Lin Kuei, is pursued by the now revived Sub-Zero, who plans to eliminate him and the remaining Cyber Lin Kuei. To his horror, Sub-Zero learns that Sektor has been mass producing a new Cyber Lin Kuei army through cloning in the Cyber Lin Kuei Assembly. After dispatching multiple cyborgs, he is captured once again by cyborg clan, fearing that he will be converted again, where he is instead brought to Sektor and Cyrax. Before the confrontation, Sub-Zero had uploaded a virus to the main computer's databanks, however Sektor tells him that the new Cyber Lin Kuei are more advanced and that the virus will not stop their programming. He is unaware that the virus did in fact free Cyrax, with him regaining his humanity, turning on Sektor and allying with Sub-Zero. After Sub-Zero kills Sektor, Cyrax gained control of the Cyber Lin Kuei, declaring Sub-Zero the new Grandmaster of the Lin Kuei and setting himself to self destruct, killing himself and the rest of the cyborgs in the factory. With Sektor killed and the factory destroyed, the Cyber Lin Kuei would come to an end, with the Lin Kuei's honor being restored by Sub-Zero.
Despite this, a single remaining cyborg named Triborg would be the last of the Cyber Lin Kuei and the Cyber Initiative as a whole. He currently seeks genocide to all life and wishes to restart the Cyber Initiative program under his command while also leading a cyborg clan of assassins of his own known as the Tekunin.
The Cyber Lin Kuei would once again return due to the time disruption caused by the Keeper of Time, Kronika. Sub-Zero, with the help of Scorpion would infiltrate the previously destroyed Cyber Lin Kuei Factory that was restarted by a time-displaced Sektor. While inside, they discover that Frost has undergone the procedure and become cyberized in her allegiance with Kronika who also appointed her the new leader of the Cyber Lin Kuei after being exiled by Sub-Zero for her assassination attempt on Scorpion. Inside, they manage to disable Cyrax's emotional and behavioral inhibitors despite being attacked by both Frost and Noob Saibot, who had also allied himself with Kronika. With Cyrax on their side once again, they plan to shutdown the factory, however they are confronted by a time-displaced Sektor. Sektor is defeated and severely damaged in the fight. Cyrax, who is linked to the Cyber Lin Kuei's network in the factory, shuts it down but ends up disabling himself in the process. Despite this victory, this would not be the end of the Cyber Lin Kuei.
The remaining cyborg clan would regroup with Geras. Sektor would be rebuilt by Kano and his past self along with the construction of remaining Cyber Lin Kuei. They would infiltrate the Special Forces Desert Command with both Kanos, a younger Erron Black along with other Black Dragon mercenaries, however Sektor is double crossed when Kano sets him to remote detonation to destroy the base after they capture the past versions of Johnny Cage and Sonya Blade. Frost would continue to lead the remaining Cyber Lin Kuei in a defense of Kronika's Keep and board some of Kharon's fleet in an attempt to stop the invading Earthrealm and Outworld forces. The Cyber Lin Kuei would finally fall after Raiden shorted Frost's circuits, disabling both her and the entire Cyber Lin Kuei army.
With the timeline being altered once again, Fujin, Nightwolf and Shang Tsung encounter the still active Cyber Lin Kuei on their quest to steal Kronika's Crown to prevent the destruction of the timeline and of all reality as a whole. Frost and Geras are accompanied by her Cyber Lin Kuei in the Shaolin Trap Dungeon to confront Nightwolf and Shang Tsung, however Frost and her Cyber Lin Kuei are defeated by the duo, with Geras following them in defeat after an assist from Fujin. What happens to Frost and the Cyber Lin Kuei is left unknown as they are not seen after this, nor are they seen supporting the Oni at Kronika's Keep in the altered timeline.
- Sektor (former Leader in both Timelines, deceased in both Timelines)
- Cyrax (deceased in both Timelines)
- Smoke (formerly in 1st Timeline, currently Revenant serving Quan Chi and Shinnok in 2nd Timeline)
- Kuai Liang (formerly in 2nd Timeline, currently Grandmaster of Lin Kuei in 2nd Timeline)
- Unit 5
- Frost (Current Leader in altered 2nd Timeline, status unknown in 2nd Timeline)
- The only Lin Kuei assassin that was never turned into a cyborg as part of the Cyber Lin Kuei whatsoever was Bi-Han who was later resurrected as Noob Saibot by Quan Chi due to being killed by Scorpion before the Cyber Lin Kuei started to form.
- Kuai Liang replaces Smoke in the 2nd Timeline due to Raiden's interference, resulting in Sub-Zero being cyberized and part of the Cyber Lin Kuei.
- This would result in Sub-Zero being the first Cyber Lin Kuei, and the only cyborg overall, to be transformed into a Revenant.
- Triborg was the last remaining member of the Cyber Lin Kuei until Kronika's altering of the timeline.
- Triborg is the first of the Cyber Lin Kuei with the ability to shapeshift.
- He is currently the only significant Lin Kuei turned in the Cyber Initiative whose real identity is unknown.
- Triborg's Arcade ending in Mortal Kombat X has him form his own clan called the Tekunin, the name and clan Sektor made in the original timeline after losing control of the Lin Kuei and the original Cyber Lin Kuei to Sub-Zero.
- Frost is the first of the Cyber Lin Kuei to retain her original face model as all Cyber Lin Kuei receive an entirely robotic headpiece.
- Frost is the only member of the Cyber Lin Kuei that lacks the ability of teleportation.