Quan Chi hired the Lin Kuei to find an ancient amulet, and Sub-Zero was sent to find the map showing it's location. He did not know Quan Chi hired a Japanese Ninja, Scorpion, for the same task just incase Sub-Zero failed. Scorpion and Sub-Zero encountered each other in the map room, where Sub-Zero killed him in cold blood. After Sub-Zero delivered the map, Quan Chi made good of his promise to the Lin Kuei grandmaster; the rival clan Shirai Ryu, was wiped out.
The Lin Kuei demonstrated their mercenary nature here when they placed Earthrealm in danger for personal gain. Sub-Zero was hired for another mission. This time he was to follow the directions on the map to a hidden Temple of the Elements where supposedly Quan Chi's amulet was kept. Defeating the four elemental god guardians in the temple, he found the amulet. Quan Chi took the amulet revealing that it was actually Shinnok 's amulet capable of freeing the fallen Elder God from the Netherrealm and allowing him to take over all realms.
Raiden, who had placed the amulet in the temple to protect it from people like Quan Chi, appeared and ordered Sub-Zero fix his mistake. Sub-Zero agreed and was teleported to the Netherrealm. There he tracked down Quan Chi and with the help of demon Sareena, he was able to steal the amulet back before it was used. Later it was revealed that Quan Chi crafted a fake and kept the real amulet
The Elder Sub-Zero's Last Mission
Sub-Zero was hired by Shang Tsung to compete in his Mortal Kombat Tournament. Though the Lin Kuei agreeed to this , someone else paid the Lin Kuei to kill Shang Tsung, to which they also agreed to. Sub-Zero was unsuccessful and didn't kill Shang Tsung. In this tournament he was incinerated by Scorpion. Sub-Zero's soul was sent to Netherrealm where he was stripped of his humanity and and became Noob Saibot.
The Younger Sub-Zero and Smoke
Despite losing, Shang Tsung survived the first tournament and arganized another one on Outworld as a trap for the Earthrealm warriors. Once again, Sub-Zero was sent to kill him but this time it was actually Zub-Zero's little brother who was sent as the replacement assumed the same code-name. This also explains why Smoke was in this tournament. He was a friens and a close ally of the younger Zub-Zero. Shang Tsung survived again and Zub-Aero returned empty handed. In the events leading up to Shao Khan's invasion of Earthrealm, the Lin Kuei have been a program of turning their clan members into cyborgs.
The first to volunteer for this program was Sektor, also refered to as LK-9T9. He is noteable for being the only one of the cyborgs consistently described as soulless for the rest of the series. Second was Cyrax, also known as LK-4D4. The Younger Sub-Zero and Smoke were also in line as well to be converted. Likely considering this fate was worse then death, the two fled the clan an act equal to treason. Sektor and Cyrax were sent to capture them. While Sub-Zero escaped Smoke was caught and transformed into the third (and last) cyborg warrior: Unit LK-7T2
Shortly thereafter, Shao Khan began his invasion on Earthrealm. Sub-Zero and Smoke had been marked as chosen warriors of Raiden, and their souls were spared. Sektor had no soul to take and stays true to his mission of killing Sub-Zero, but fails. Cyrax ends the game trapped in the Gobi Dessert. Smoke is later shown to have been captured by Shao Khan at some point. Noob also appears on Shan Khan's side.
Most likely due to Sub-Zero's successful escape from the clan following the events of Mortal Kombet Trilogy, the Lin Kuei lost many of it's members and is even described as "disband". Perhaps it explains their attempt to have Sub-Zero killed., because they blamed him for their troubles. Cyrax , whose souls had begun to reassert itself, was recovered from the desert by the Outworld Investigation Agency and sought out the help of Sonya Blade and Jax Briggs, who helped restore his memories and former self. After finally defeating Sub-Zero, Quan Chi reveals that he was the one responsible for the death of Scorpion's family and clan, while aslo responsible for Scorpion's own death. Scorpion responded by taking Quan Chi with him to the Netherrealm.
The storyline of Deadly Alliance revealed some significant changes to the Lin Kuei amd their history. During the events of Mortal Kombat Gold, Sektor's programming became corrupt and he attcked and killed the Lin Kuei Grandmaster. Sektor attempted to turn himself into the new Lin Kuei Grandmaster by taking possession of a hitherto unmentioned Dragon Medallion, whose possession determines the leadership of the Lin Kuei and also increases the powers of who ever wears it. Sektor was prevent from taking the medallion by a returning Zub-Zero, who fought him over the clan's leadership and won. Sektor fled to Japan and and Sub-Zero became Grandmaster.
Sub-Zero made a number of changes to the clan. He moved the Lin Kuei headquarters from its original location in China to an ancient temple he had discovered buried in the ice of the Himalayas. He also changed the mission of the Lin Kuei, making it a force for the side of good for the first time. He began recruiting new warriors to replenish the Lin Kuei's depleted ranks. Among these efforts was a tournament, the winner would be introduced into the clan.
The winner was Frost, a young woman with powers remarkably similar to Sub-Zero's own ice-controlling abilities. Frost became Sub-Zero's personal student. He was able to teach her new ways to use her powers, but failed to quell her sense of arrogence and ambition. Around this time, Sonya Blade attempted to contact the Lin Kuei at some point perhaps in the effort to open relations between the Outworld Investigation Agency and the Lin Kuei. However, she was prevented from doing so by an overjealous Frost.
Journey into Outworld
Sub-Zero realized he was unpopular with most of the members of the Lin Kuei. Therefore, he attempted to prove himself by helping Raiden fight the Deadly Alliance. The Earthrealm warriors ultimately lost against the Deadly Alliance. While in Outworld, Frost turned against Sub-Zero and attempted to steal the Dragon Medallion from him. Thiugh successful she was consumed by her own freezing ability. His trouble with Frost saved him ffrom a worse fate, as the four other Earthrealm warriors and Kitana died at the hands of the Deadly Alliance.
After Frost's apparent death, Sub-Zero searched for a place to bury her and found the ruins of an extinct civilization: the Cryomancers. They were people who could control the powers of ice and cold. Sub-Zero inferred that he and Frost both were descendents of this race. He also found an ancient armor in the tomb, and donned it. Sub-Zero decided it would be best to head back to Earth after the Deadly Alliance was defeated by the even more sinister Onaga.
On his way to the portal, he encountered Kenshi who was badly wounded. The two decided to travel together. Along his path, Sub-Zero had killed many Tarkatan warriors, drawing attention from Onaga and his enforcer, Hotaru. Once again the Grandmaster found himself marked for death. In Mortal Kombat: Tournament Edition, it was revealed that Sub-Zero also encountered Sareena in Outworld. He offered her asylum with in the Lin Kuei for helpin his older brother in the Netherrealm many years before.
Upon his return to the clan's temple in Earthrealm, Sub-Zero found that Frost had awakened and returned to slay him. In her rage, she saw Sub-Zero everywhere and had already killed many of the Lin Kuei members. Sub-Zero froze her and put her body on an alter, sealing off the room with a wall of ice until she can one day recover.