Hundreds of years ago, there existed a clan of thieves and assassins known as the Lin Kuei. They did the bidding of those who paid top dollar for their services, without any regard of the consequences. Generally speaking, membership of the Lin Kuei lasts from cradle to coffin. Their members were chosen from birth, taken away from their families and trained to be ruthless killers, and leaving the Lin Kuei was considered tantamount to treason, and therefore was punishable by death (in other words, the only true way out of the clan is death). One assassin learned the latter the hard way. He was a Japanese-born Lin Kuei assassin by the name of Takeda, and upon returning to his homeland, he used the skills he learned in the Lin Kuei to develop a new artform known as Ninjutsu. Instead of relying on supernatural abilities, ninjas use magics and skills that can be mastered by any ordinary human with enough practice. The ninja did not exist as one big clan, but as a loosely-connected spy network consisting of many different clans. One of those clans was the Shirai Ryu, which was founded by Takeda himself. Since their founder was a deserter of the Lin Kuei, the Shirai Ryu as a whole, and Takeda in particular, was marked for death by the Lin Kuei. Takeda evaded his former clan for many years, until his elder years, when he died not in kombat, but in his sleep, the victim of poison slipped into his tea. It has never been made clear who was responsible for Takeda's death, but given the Lin Kuei's obvious stance on desertion, and the time and resources they spent on trying to take him out, it is speculated that the Lin Kuei was behind it.
The war between clans continued for centuries, until the vile Netherrealm sorcerer Quan Chi, with ulterior motives, sent members of both clans to a Shaolin temple to steal an ancient map. Representing the Lin Kuei was Bi-Han, code-named "Sub-Zero", who was a 5th generation member of the Lin Kuei who had mastered the arts of cryomancy, a skill hereditarily passed to him by his ancestors. Representing the Shirai Ryu was a ninja of at least the second generation named Hanzo Hasashi, code-named "Scorpion", who by this time mastered the use of the kunai and shurikens. While Bi-Han and his younger brother were chosen by their father to join the Lin Kuei, Hasashi was forbidden by his father from joining the Shirai Ryu. Apparently, the elder Hasashi must have experienced enough bloodshed and treachery to know that he did not want his son to live this same life. Nevertheless, Hanzo was tempted to join his father's clan to provide a better life for his wife and child, and joined the clan anyway. As Quan Chi anticipated, the two rivals engaged in a heated battle where Bi-Han slew Hasashi and completed the mission on behalf of the Lin Kuei. During that time, Quan Chi slaughtered every last remnant of the Shirai Ryu, even going as far as eliminating the surviving families of each member (as evidenced by the fact that Scorpion's wife and child were killed). However, the sorcerer had an ace in the hole. He framed Bi-Han and his brother Kuai Liang (the latter of whom was at the time code-named "Tundra"), in the event that he was betrayed by either of them, or by the Lin Kuei as a whole. Additionally, he resurrected Scorpion as an undead specter to unleash his vengeance should it come to that. As it turned out, Bi-Han DID betray Quan Chi, as Raiden guilt-tripped Bi-Han into taking back Shinnok's amulet from the sorcerer. After the amulet was brought back to Earthrealm (although this later proved to be a ruse as Quan Chi made a fake while keeping the original in an act of conning Raiden, and possibly double-crossing Shinnok), he used Bi-Han's framed role in the Shirai Ryu Massacre against him by sending Scorpion to the Mortal Kombat tournament.
During the tournament, Scorpion got his revenge and slew Bi-Han, who was later resurrected by Quan Chi as the undead wraith Noob Saibot, but Scorpion did not know that Sub-Zero left behind a younger brother. Kuai Liang, sensing something wasn't right after his brother failed to return from the tournament, went into Outworld to attempt to finish his brother's mission of assassinating Shang Tsung, but also had intentions of investigating his brother's disappearance, and to honor his brother's memory, Kuai Liang ceased to be known as Tundra and adopted his brother's code-name. Well, Scorpion somehow found out about Sub-Zero's return, and sought answers as to how someone he killed with his own hands and saw die with his own eyes could be back...both were oblivious to the circumstances until they crossed paths. Sub-Zero had learned of his brother's fate from Earthrealm witnesses, while Scorpion witnessed Sub-Zero spare the life of a defeated enemy, which cast doubts as to his identity in his mind, later finding out that this Sub-Zero was in fact the younger brother. Aware that his own family was taken from him and that he had done the same to someone else, Scorpion is believed to have become Sub-Zero's guardian in atonement for killing his older brother. This newfound loyalty would be tested when he was recruited by Shao Kahn to take part in the invasion of Earthrealm, only to find out later that Sub-Zero was among the Earthrealm warriors chosen by Raiden to defend the realm from Kahn's treachery, and therefore a target for death by Kahn's extermination squads (it is unclear if Scorpion knew that Sub-Zero had deserted the Lin Kuei and as a result was marked for death by that clan as well, as was the case with his own clan's founder). Scorpion stayed true to his oath towards Sub-Zero and betrayed the emperor without regard for the consequences, but Scorpion's loyalty to Sub-Zero would be short-lived. Quan Chi masterminded another attempt at getting Shinnok out of the Netherrealm and waging a war against the Elder Gods who banished Shinnok. Hoping to recruit Scorpion and finish his revenge on Sub-Zero, Quan Chi used Kuai Liang's framed role in the Shirai Ryu Massacre to turn Scorpion against Sub-Zero. The ruse worked, and Scorpion defeated Sub-Zero, but as he was about to finish off the former Lin Kuei assassin, Quan Chi made the mistake of revealing his treachery to Scorpion. Needless to say, Scorpion was PISSED that he had been lied to the entire time, as he not only took his frustrations on two people who were completely innocent of such a heinous massacre, but that the TRUE killer of his clan, wife and child was the same one he had been serving in the first place. Scorpion restored his oath never to harm Sub-Zero, and this time, it was permanent...the target of his wrath was now Quan Chi.
Scorpion spent the next ten years tormenting Quan Chi in the 5th plane of the Netherrealm, where Scorpion's power grew stronger and Quan Chi's got weaker. However, Quan Chi would soon discover that the amulet he had stolen would soon get him out of a world of shit. He opened a portal into Outworld, and masterminded a plot to take over Outworld, as well as other realms (the process of which involved forming an alliance with Shang Tsung and the assassinations of both Shao Kahn and Liu Kang). Scorpion didn't give a shit what Quan Chi was up to, only as long as he got his revenge. Scorpion found himself thrown into Shang Tsung's soulnado, and was nearly ripped apart by the purity of the heavens, but Scorpion escaped and found himself standing before the Elder Gods themselves, who transformed him into their champion to stop any threats to the stability of the Realms. As it turns out, Onaga, the former emperor of Outworld who was known as the Dragon King in his prime, had been reborn at around this time and sought to finish what he started thousands of years before; merge the realms and destroy the Elder Gods. Scorpion played a role in Onaga's defeat, and as repayment for his services, the Elder Gods resurrected his clan and family...the catch being that they would be just as alive as him. This enraged Scorpion, so he betrayed the Elder Gods and sought to destroy ANY forces of light...including Taven, who was on a quest to stop Armageddon.