The Mishima Zaibatsu headquarters was under attack from the U.S Military Special Forces, and most of the staff had been arrested already. Nina Williams, one of the last people in the building, was attempting to escape through a hidden exit that only her and Jin knew about. As she was about to run to the hidden door, she saw shadows of several soldiers coming around the corner towards her. She quickly hid herself in a small side corridor that she knew only led to an elevator and an empty vending machine. She waited for the last member of the team, that member being Lieutenant Sonya Blade, and grabbed her silently from behind, holding a knife to her throat and backing away down the hall the soldiers turned and pointed their guns at her.
"Back off, or she dies!" Nina ordered, making a cutting gesture with the knife.
"Like hell!" Sonya snapped, struggling against Nina's grip, and much to Nina's surprise, breaking free and grabbing her, a short power struggle between the two ending in them forcing each other out of a twelfth story window onto a balcony workers used to smoke where they thought they couldn't be seen.
The two women then pushed each other back and Sonya shot at Nina a few times with her energy ring. Nina was hit once, but managed to dodge the next attack and attempted to run in at Sonya, which proved to be a mistake, as Sonya used her Arc Kick to leap towards the assassin and catch her in the face, sending her to the metal ground and shaking the shoddy balcony. She attempted to hit Nina while she was down, but the assassin trapped Sonya's legs in between hers and sent her to the ground. The two attempted to hyperextend the other's leg, but neither prevailed and they separated once again. They got up and fought each other in hand-to-hand combat. It was close, but Sonya's skill proved to outmatch Nina's, landing several blows on occasion and finally countering the assassin's attack, unleashing a combo on her, knocking her back.
"Not bad." Nina said, wiping a small sliver of blood from her mouth.
"Just getting started." Sonya said, re-engaging into her fighting stance.
The two fought again, charging at each other and exchanging blows. Nina's strength gave her a small advantage, but Sonya's skill and technique proved to be more than enough to balance out that advantage. The two eventually pushed each other back. Nina then rolled forward, did some type of flying uppercut to Sonya, spun like a helicopter propeller, smacking Sonya in the face a few times, then hitting her in the chest with both palms, blasting her to the ground with a strange energy (her Super Move from Street Fighter X Tekken). Sonya quickly got up, having been in better shape than Nina when the attack happened, so she could keep going, saw Nina was now open after unleashing the attack and hit her with her own, a left backhand slap, a right haymaker, left round kick and right stomp to the back of Nina's head, then did a handstand and grabbed the assassin's head in between her legs. She then twisted her legs and Nina's head, horribly damaging her neck and even breaking off pieces of the vertebrae in Nina's neck, then used her own version of Liu Kang's bicycle kick to kick Nina into the air a few feet, then grabbed her under the arms with her leg and smashed her head into the ground, cracking her skull and knocking the formidable assassin unconscious.

"Lucky for you we need more information on the Zaibatsu. You're coming with me." Sonya said, collecting Nina and throwing her over her shoulder.

"Sonya, grab on." Jax said, tossing a rope down to her.

She climbed up and saluted her C.O. "Thanks, Jax. Let's get her back to base, she's got to know more about the zaibatsu and Jin than most of the other people here do." She said.

Reasons for the outcome:

1: Mortal Kombat specifically said she quickly rose up to the rank of lieutenant in the Special Forces, which, while Lieutenant is a relatively low-rank, being in the special forces requires the elite to begin with, if she gained ranks at a rapid pace, that means she is highly skilled and elite, as it takes most others years on some occasions to improve one rank. Nina was basically given her place at Jin's side. There is a clear line between being given a rank and earning it.

2: Sonya was able to defeat two top Outworld assassins together on her own, then Kano shortly after. Nina is never shown to take on multiple elite soldiers at once, only Anna which is usually an even match that often leaves her tired after winning, presumably unable to take on another opponent.

3: Sonya has undergone rigorous military training, followed by even more difficult training in special forces, giving her an edge in skill. Nina has an advantage from being enhanced during cryosleep, making her possibly stronger and faster, but skill usually trumps all of those.

4: While you cannot deny Nina is skilled, her only real training came from her father, who died when she was around 8, so she could've only had a few years at most to learn the skills she had, where, once again, Sonya has had constant and rigorous training and can always go back for more if needed, putting her skill above Nina's.

5: Sonya's got more gadgets and maneuverability to put the battle in her favor and can keep Nina at a range if needed, giving her yet another advantage, as Nina relies on close-range combat.

6: I also have to give the edge in durablitiy as she survived Sindel's slaughter or the guardians of Earthrealm and a blast from Shao Kahn, both of which would easily kill any normal human. Nina has never been shown to have incredible endurance, only speed and power.

7: Sonya fights numerous monsters, whereas Nina doesn't. Nina may be destroyed if she takes on Sub-Zero or Kitana, both of whom could be defeated by Sonya.