In life, Scorpion was the codename for a human ninja assassin and one of the Shirai Ryu clan's finest warriors: Hanzo Hasashi. It is also known that his father, a former member of the Shirai Ryu, forbade his son from joining the clan, as he did not wish his son to live the life of an assassin. However, Hanzo joined in spite of his father's wishes in order to provide his wife and son with a comfortable life.

Storyline

Two years after being slain by the elder Sub-Zero, Scorpion returned to Earthrealm and participated in Shang Tsung's tournament. However, it would not be until after Liu Kang's defeat of Goro that he would catch Sub-Zero unguarded and have his revenge, burning the defeated Lin Kuei to death. Immediately afterward, he returned to the Netherrealm in an explosion of fire and ash.

While in the Netherrealm, Scorpion would catch wind of a new tournament in Outworld, as well as Sub-Zero's participation. Shocked and angered that his murderer somehow returned to life, Scorpion followed his opponent to Shao Kahn's tournament. However, during one of Sub-Zero's battles, he witnessed the Lin Kuei sparing his opponent's life. He would soon learn that this Sub-Zero was not his murderer, but Sub-Zero's younger brother. To atone for slaying his kin, Scorpion vowed to protect Sub-Zero instead. But Sub-Zero would never know this, or the reason behind it.

When Shao Kahn invaded Earthrealm and unsuccessfully tried to conquer the Netherrealm as well, Scorpion was inadvertently set free, and began walking the Earth once more. He pledged allegiance to no one, taking neither friends nor enemies. Shao Khan, however, recognized Scorpion's superior warrior skills, and enlisted the ninja in his forces. Scorpion's allegiance with Shao Khan quickly dissolved when he discovered that Sub-Zero was one of Earth's Chosen warriors and therefore one of Shao Kahn's targets. He turned on Shao Kahn, and sided with the Earthrealm warriors in their final showdown with the evil emperor. With Shao Khan and his minions defeated, Earth reverted back to normal, causing Scorpion to return to the Netherrealm once more.

Sometime after his return to the Netherrealm, Scorpion heard that his wife and child had been slain. He encountered the sorcerer Quan Chi, who told Scorpion that Sub-Zero was the murderer. Hearing this angered Scorpion anew, and he swore he would slay Sub-Zero, much like his brother before him. However, during Shinnok's invasion events, Quan Chi reveals that he had tricked Scorpion into believing that Sub-Zero had slain his wife and child in the hope that he would break his vow of protecting Sub-Zero as retribution for killing his brother the original Sub-Zero. The true murderer of Scorpion's family was Quan Chi. After Scorpion defeated the new Sub-Zero and learned the truth, the sorcerer attempted to transport Scorpion back to the Netherrealm. Thinking quickly, the spectre ran towards the sorcerer, sending both of them back to the Netherrealm.

During the years that Quan Chi spent trapped in the fifth plane of the Netherrealm, he would be chased, brutalized, and tortured by Scorpion. Quan Chi had little chance of escape, as his powers were weakened while he was in the Netherrealm, and Scorpion's power and strength conversely increased (note: Quan Chi, as Shinnok's second-in-command, had previously resided in the Netherrealm. However, this was explained as a new region of the Netherrealm where sorcerers retain their power). Quan Chi eventually struck a deal with the Oni Drahmin and Moloch, who fought off Scorpion for him. When Quan Chi escaped the Netherrealm through a portal, Scorpion followed him, but it did not send him to the same place. He continued to hound Quan Chi in a game of cat-and-mouse until he found himself at Shang Tsung's palace, where he was ambushed by Drahmin and Moloch, who had also escaped the Netherrealm. They threw him into the Soulnado, believing that it would eliminate the ninja spectre once and for all.

Scorpion, however, managed to escape into the Void before the purity of the soulnado tore him apart. While in the Void, he met the Elder Gods, in whom he had never believed, and forever became changed from what he saw. He also witnessed Raiden's sacrifice and Onaga's dominance beginning to unfold. The Elder Gods were aware of his presence and enhanced his mortal and supernatural abilities, making him the Champion of the Elder Gods. The Elder Gods gave him a new mission, to seek and destroy Onaga before he unmade the realms. Scorpion emerged from the Void and returned to Outworld. Scorpion is seen in Konquest mode before Onaga goes to retrieve the amulet from Quan Chi and fights Shujinko in the name of the Elder Gods. Shujinko won the battle.

Scorpion was no longer willing to serve as the Elder gods' champion. This was due to the bargain he had made with the Elder Gods to serve them in the first place; they would resurrect the Shirai Ryu clan along with the ressurection of his wife and son, in return for his services. While the Elder gods did fulfill their promise, they brought back the Shirai Ryu clan as hellspawned warriors, the same as Scorpion. Enraged at what he perceived as their betrayal, Scorpion vowed to gain vengeance on the Elder Gods by removing the two things crucial to their plans to prevent Armageddon - the Edenian brothers Taven and Daegon. As Taven made his way to a final confrontation with his brother, Scorpion's clan repeatedly attacked him. With his warriors unable to stop the half-god, Scorpion used his powers of the Nether and summoned giant, flaming skulls to attack Taven. Yet again, Taven prevailed, leaving Scorpion to fight him, but the ninja spectre lost.