During the Earthrealm invasion, Sub-Zero appears in his upgraded form as Cyber Sub-Zero. He attacks Kabal but is defeated. At Smoke´s request, he is brought to Jax, who removes the slaving protocols in his CPU, giving him his free will back. He regrets all the things he did for Shao Kahn, so he joins them and goes to spy on Outworld. After a brief discussion, Sektor orders Sub-Zero to go on a mission with him. He informs Sub-Zero that he scanned his neural net, and knows he has been reprogrammed. Sektor ordered him to open his access panel, but he attacks him instead, starting a fight between the two, which Sektor loses.

By searching in the defeated Sektor's data banks, he discovers the location of Kano, Kintaro, and Goro. He finds the three of them in the Bell Tower torturing soldiers. After a failed attempt to get information, he freezes the three of them, and frees the soldiers. After they escape, Kintaro and Goro break free of the ice they were trapped in, leaving Sub-Zero to fight both. He does, and emerges victorious. The freed soldiers are then pushed back by Ermac. Sub-Zero warns them to stay back, then fights and defeats him. After asking the soldiers their next location, he goes to the graveyard. The soldiers wish him good luck, another jokingly saying he didn't need it.

In the graveyard, Sub-Zero comes across Quan Chi and Noob Saibot as Chi conjures up a spell to create a Soulnado. When he confronts Noob, he discovers that Noob is his older brother. After Noob relinquishes any family ties with him, they fight, with Sub-Zero emerging victorious, and claiming that he was right; they are no longer brothers. At Nightwolf´s advice, he reports back to Raiden. When Raiden leaves with Liu Kang to try to talk to the Elder Gods, he is left under Nightwolf´s command. Some seconds later, he detects the Lin Kuei Cyborgs, then they are ambushed. After they dispatched the Cyborgs, Sindel appears and states that she "will finish what the Lin Kuei did not". The Earthrealm warriors engage her in battle, and he, along with most of them, is killed when Sindel destroys his circuits. He is later resurrected by Quan Chi to serve him in the Netherrealm.