Mileena has been tasked by Shao Kahn to keep watch over her "sister" since lately she has been acting strange and Kahn suspects she is up to something.
Mileena has been keeping a close on eye on Kitana eager to prove her worth to her father. She is careful in making sure Kitana does not notice her. She then catches her conversing with the Earthrealmer and new champion of Mortal Kombat Liu Kang in the living forest. She overhears Kitana telling Liu Kang about Shao Kahn's planned invasion of Earthrealm and how a "revival" will allow him to do it. Finally catching her in the act Mileena then sneaks away to relay this new information to their father. Unfortunately, Kitana notices her leaving and puts two in two together and tells Liu she will meet up with him and the other Earthrealmers later and chases after Mileena.
After a brief chase Kitana catches up to Mileena and they circle each other. Mileena tells Kitana she knows what she has been doing and will pay for this betrayal. Kitana seeing no other way charges Mileena, and a fight begins. Mileena is trying to cripple her to bring her to Shao Kahn and Kitana is going for the kill.
During the fight they briefly stop to catch their breathes and Kitana tries to appeal Mileena and tells her that no matter what she does Kahn will never love her because she is a failed clone. Mileena refuses to hear this claiming she is NOT a clone, and it is just because of her face that he doesn't yet love her.
Seeing this Kitana thinks maybe thinks maybe she can turn Mileena. Kitana has been hesitant on turning on Shao Kahn because she knows how powerful he is and what could happen if he catches her. She thinks if she can turn Mileena she might not have to go through this alone. Her reaction to being called a clone leads her to believe that they are more alike than she thought and Mileena is just as much a victim of Kahn as she is. Perhaps this whole time she really did believe she was Kitana's long lost sister only to find out she is not, just like how Kitana thought Shao Kahn was her father when it turns out he murdered her real father. Both have been lied to and have reasons to hate him.
With this in mind Kitana shows pity to Mileena as she has started to cry and offers her a hand asking her to join her in turning against Kahn. She tells Mileena it is not too late for her to change just like she has. Mileena looks up with tears running down her face and asks of she really believes that. Kitana says she does since a part of Mileena is still her and if she can change for the better than Mileena can as well. Mileena slowly takes her hand and agrees to join her.
Happy with this development Kitana turns to lead Mileena to her new allies. She is talking about how this is a huge risk but for some reason she believes they will be successful in this and will be rid of Kahn forever. However, Mileena is silent while she is talking and uses the opportunity to clock her over the head while her back is turned. Kitana crumbles to the ground unconscious. Mileena stares at her and says how Kitana is wrong about Shao Kahn and will prove it.
She takes the unconscious Kitana to her room and uses rope to tie her up and hides her in her closet. She then takes Kitana's mask and smears it with blood and leaves. She returns to her father and he questions where she has been and if there are any updates on Kitana. Mileena proudly shows him Kitana's blood-stained mask and tells him how she caught her conversing with the champion Liu Kang and how she was planning on betraying them. She confronted her and killed her for this and through her body onto a living tree. Mileena waits to be congratulated for this but is horrified by the reaction she gets.
Shao Kahn is furious with this and Mileena has never seen him this angry before. He is even more angry than he was at Shang for losing the tournament. Mileena tries to calm him down reminding him that Kitana was planning on betraying them, has been for years. Shao Kahn yells at her and says she still could have been brought back to their side. He furiously calls Mileena a failure in that he ordered her to just WATCH Kitana and report back to him if anything was of and she cannot even do that properly! He rants about how because of this failed abomination his true daughter is now lost and that he knew Mileena's creation was a mistake and should have told Shang Tsung to dispose of her just like the rest of the failures before her.
This completely devastates Mileena, and a horrible realization comes to her. Kitana was right. She was right about everything. She doesn't have a lot of time to dwell on this since Kahn in rage rushes to Mileena and lifts her by the throat choaking her. Mileena takes her sai and desperately stabs his arm but to her horror it breaks. Wearing and knowing death is coming Mileena takes her last sai and throws at across the room and once it embeds itself in the wall, she gets teleported to it and rushes out of the throne room. Kahn deems her a traitor and orders his guards to hunt her down and bring him to her alive so he can torture her.
Kitana has come to and is surprised to see she has bound and gagged. She is furious and figures Mileena did this. How stupid of her to believe her "sister" could change. For as long as Kitana has known her Mileena has always been eager to prove her worth to their stepfather and proving she was better was how she believed she could get Shao Kahn's approval. She starts to struggle to break free of her ties, but they are too tight. She stops her struggling when she hears movement outside the door and glares as Mileena is the one to open the closet door. Kitana glares at her clone with defiance. If she is to die her and now, she will not give her the satisfaction of seeing her scared. Mileena approaches her with her sai raised and Kitana accepts her fate.
What comes next left her confused. Instead of stabbing her Mileena uses her sai to cut the ropes restricting her. Once they are all cut, she backs away and slides to the floor leaning against Kitana's bed. Kitana for the first time notices the lost look in Mileena's eyes and bruise around her neck. She cautiously stands and demands to know what is going on. Mileena is silent and just stares ahead, not really looking at anything and then begins to cry. Kitana is unsure what to do here and just stares at her and waits for Mileena to finish.
After a few minutes of crying Mileena with her face buried in her knees tells her she was right. She tells Kitana of what she did and how Kahn reacted. Having said it out loud she starts crying again and starts to fall into depression. She had spent years believing he would give her the love she wanted if she pleased him. Believing if she proved she was better than her sister he would finally accept her. While out on missions she was unnecessarily brutal to the people of Outworld in the hopes her brutality would gain his approval. So many years wasted and after hearing him say her creation was a mistake only further crushed her.
Kitana is unsure if she should believe her clone. She believed her once before and she betrayed her. Had her plan worked out Mileena would have gladly killed her once she was proven right. But seeing the sheer emotion in Mileena once again fills her with pity and realizes she needed to see for herself the kind of man Kahn is. But if everything Mileena said is true then Shao Kahn really does love her and Kitana questions why. This whole time she believed he kept her as an insult to her father but to find out he genuinely cares about her gives her even more questions.
Standing before Mileena Kitana once again offers her the chance to join her and her allies on turning against Kahn. Mileena looks up with even more tears on her eyes and take Kitana's hand and this time she is serious. She finally accepts that Kahn is the one who ruined her and made her feel inferior her entire life. Seeing what kind of man, he is Mileena vows to destroy Shao Kahn's legacy.
Kitana asks Mileena how she got here if she has been branded a traitor and Mileena tells her she snuck in through the window. Kitana insists Mileena goes first and Kitana decides to use the fact that everyone now believes she is dead to her advantage.
With a strong resolve Kitana and her sister Mileena escape the fortress and meet up with the earth warriors.