Later, Smoke and Jax are attempting to reprogram Sub Zero. What Cyber Sub Zero could see is black which stays like that for a moment, and all that can he can hear is the background noise of diagnostics. Then the word "_INITIALIZING" pops up on his screen.

"That's it. Here goes nothing..." Jax says.

Sub Zero's mainframe then begins rebooting, all of which he sees from his point-of-view.

"You are certain this will work?" Smoke asks.

"Hell no! I've never done this before. It's not like there's a manual." Jax replies.

Sub Zero's screen is then suddenly lit up in red. The word "OVERRIDE" shows up in enlarged text. It successfully engages, and Sub Zero tries connecting to a wireless uplink. The connection fails and an error pops up, noting his command and control module is missing. With that, his slaving protocols are disengaged and his autonomous command module is engaged, restoring his higher brain function. Smoke looks directly into his eyes at this point.

"Sub Zero?" Smoke asks Sub Zero.

He then turns toward Jax. "Can he hear me?" Smoke asks.

"He should." Jax says.

Sub Zero then locks onto Smoke's eye and does a retinal identification.

"Sub Zero?" Smoke asks.

The scan provides Sub Zero with information about Smoke, including his age, country of origin, his allegiance and special ability.

"Yes, Smoke." Cyber Sub Zero answers.

"How do you feel?" Smoke asks.

It is now clear that the heroes are currently in some kind of temple. Cyber Sub Zero then sits up on the slab he's been placed on. He grunts in displeasure.

"What is it?" Smoke asks.

"I remember... The things I have done for Shao Kahn..." Cyber Sub Zero replies.

Smoke then places a hand on his friend's shoulder.

"He cannot be allowed to merge the realms." Cyber Sub Zero says.

Nightwolf then turns to Raiden.

"Haokah, how can Sub Zero best help us?" Nightwolf asks.

"I do not know. My attempts to alter future events have had negative consequences. Sub Zero should never have undergone this transformation. Enlisting him may only further divert the flow of time." Raiden says.

"We need intel, right? Let's send him back to Outworld undercover." Stryker suggests.

"They will be unaware of my defection. I could deceive them." Cyber Sub Zero says.

Raiden considers this in silence.

Later in Shao Kahn's throne room. Sektor and Cyrax are conversing with Noob Saibot, while several Tarkatan minions await orders. A portal has been opened and Cyber Sub Zero walks through it.

"Earthrealm is finished. It will not be missed." Noob Saibot says.

"Very well. You will return." Sektor says.

Noob and Cyrax then walk off into the portal, with the minions following. Sektor then turns to Sub Zero.

"You report late. Where is the intruder?" Sektor asks, seeing that Kabal is nowhere to be seen.

"I killed him in Earthrealm." Cyber Sub Zero replies.

"He should have been saved for interrogation." Sektor says.

"He was formidable. I had no choice." Cyber Sub Zero says.

"Follow me. We must lead a new mission." Sektor informs.

Sektor then walks into the portal and Sub Zero follows.

They then emerge in the Subway where Stryker fought Ermac.

"What mission brings us here?" Cyber Sub Zero asks.

"I have scanned your neural net, 5-2-0. Your neuromodulators have been recalibrated." Sektor says.

"Impossible." Cyber Sub Zero says.

"The experience has been deleted from your system. Remove your access panel." Sektor demands.

As Sektor moves in, Sub Zero grabs his wrist and palm-strikes him in the chest, sending him careening across the platform.

"Your programming has been corrupted." Sektor realizes.

"My soul was corrupted. Now it is cleansed." Cyber Sub Zero says.

They then fight. Sub Zero would have been a match for Sektor even without his cybernetic upgrades; with them, the match is one-sided and ends quickly with Sektor's systems being knocked offline.

"Artificial enhancements are no substitute for the human soul." Cyber Sub Zero says.

Sub Zero then walks over to Sektor's inert form and accesses his mainframe. As he hacks into the system and discovers Sektor's true orders, Sub Zero sees that they are to escort military prisoners from Vogel University to St Dominic's Cemetery for processing, with uncooperative prisoners being expendable. Sub Zero also finds the path being taken from the station to the university and the cemetery.

"Thank you, Sektor." Cyber Sub Zero says.

In the clock tower of St Dominic's Cemetery, eight army soldiers are currently being kept prisoner, with Kano, Goro and Kintaro watching over him. Kano takes the opportunity to blast the soldiers with his eye laser, laughing as he does so.

"Oy! Run about, will ya?" Kano asks.

Cyber Sub Zero then enters the clock tower.

"Finally! C'mon, we gotta get 'em to the graveyard at Saint Dominic's. On yer feet, all of ya!" Kano informs.

"For what purpose?" Cyber Sub Zero asks.

"Don't care, really. So long as I get paid." Kano replies.

"He said on your feet!" Kintaro orders.

"C'mon, up!" Goro yells.

"Get up!" Kintaro also yells.

Suddenly, two ice blasts freeze Goro and Kintaro where they stand.

"Hey! What're–" Kano says before Sub Zero then freezes him with an ice blast as well and then turns to the soldiers.

"I will help you." Cyber Sub Zero assures.

He then takes a hold of the chain shackling the soldiers together and freezes it. He punches the frozen chain and it shatters completely, freeing the soldiers. Goro and Kintaro begin breaking free of the ice they are bound in.

"Go! All of you! Now!" Cyber Sub Zero orders.

"Let's go! C'mon!" One of the soldiers says.

The soldiers then make their escape just as Goro and Kintaro break free of the ice.

"Your treachery will be punished!" Kintaro says.

They then fight. Facing both Goro and Kintaro at once would be impossible odds for any normal human, but Sub Zero was no ordinary human even before he was turned into a cyborg. Nonetheless, the fight is one of the most difficult of his life, but eventually he prevails against the Shokan warriors.

"All those teeth and claws, yet still overmatched." Cyber Sub Zero says.

Suddenly, the clock tower starts shaking, causing the bells to ring. A burst of green light then appears near the exit and all the soldiers seen before are all telekinetically tossed back into the room.

"Behind me!" Cyber Sub Zero calls out.

The soldiers struggle to their feet and comply as Ermac floats into the room.

"Come no further, fiend of Outworld!" Cyber Sub Zero demands.

They then fight. Not even Shao Kahn's personal enforcer is a match for Cyber Sub Zero, and the red garbed ninja is soon defeated by the cyborg.

"You are not so fearsome." Cyber Sub Zero says.

With Ermac down, the soldiers surround and congratulate Sub Zero.

"Thanks. I thought we were done." Soldier 1 says.

"I must go. I need to investigate the graveyard." Cyber Sub Zero says.

"We'd go with, but we have to return to our unit." Soldier 2 informs.

"That is for the best." Cyber Sub Zero replies.

The cyborg then leaves immediately.

"Good luck, man." Soldier 1 calls out.

"He ain't gonna need luck." Soldier 2 says.

In the cemetery, Noob Saibot is magically drawing two lines across the ground, creating a ring around another captured group of soldiers. Quan Chi is nearby, chanting a spell in a NetherRealm tongue. Cyber Sub Zero is kneeling by a gravestone, undetected by neither of them. The soldiers surrounded by the ring begin to glow green with the rising energy around them. Sub Zero then speaks into a wrist-communicator.

"This is Sub Zero. I have encountered Quan Chi. He seems to be casting a spell." Cyber Sub Zero informs.

Back at the temple, Sonya has her wrist-comm on speaker for the Forces of Light to listen in. Raiden then receives another vision, this one of a Soulnado engulfing New York City.

"Raiden, what is it? What did you see?" Nightwolf asks.

"One of Shao Kahn's Soulnados, on a scale I thought unimaginable. All of Earthrealm's souls imprisoned, absorbed by Shao Kahn, multiplying his power!" Raiden explains.

"That is what Sub Zero has found?" Nightwolf asks.

Raiden then looks at his amulet. More cracks and a burnt signature adorns it.

"No matter my efforts, the future remains in peril. How could I have failed Earthrealm?" Raiden asks himself.

"Do not lose faith in the spirits, Raiden. They will guide you. Protect you. Sub Zero, we will disrupt the Soulnado. I will be there momentarily." Nightwolf says.

"Hurry. The spell appears to be nearly complete." Cyber Sub Zero informs.

Sub Zero then stands from his hiding place and walks into the clearing.

"Who is that?" Quan Chi asks, noticing Sub Zero.

"The one Kano warned about. He is mine." Noob Saibot replies.

Noob Saibot then walks toward Sub Zero.

"You. You are not worthy of the name Sub Zero." Noob Saibot says.

"Who are you to judge?" Cyber Sub Zero asks.

"I wore those colors before you." Noob Saibot answers.

"Bi Han?!" Cyber Sub Zero asks in shock, realizing that his brother is right in front of him.

"Yes, Kuai Liang. It is I. Quan Chi restored me." Noob Saibot replies.

"Restored? You and I both. We are flawed copies of our former selves." Cyber Sub Zero says.

"I have no flaws. Quan Chi has perfected me." Noob Saibot says.

"For what end? To serve the Netherrealm and Outworld?" Cyber Sub Zero asks.

"It suits my purpose." Noob Saibot says.

"But brother, we–" Cyber Sub Zero tries to say before being cut off.

"We share blood. We are not brothers." Noob Saibot says.

"Then I will not regret your defeat." Cyber Sub Zero says.

They then fight. Bi Han may have had power granted to him from the Netherrealm upon his death, but Kuai Liang's cybernetic upgrades prove to be superior in battle. After a fierce battle, Kuai Liang manages to defeat his brother and leave him unconscious.

"You are right. We are not brothers." Cyber Sub Zero says.