Spoilers: (Highlight to reveal)
Mileena deceives the entire Edenian/Outworld rebellion army that she is Princess Kitana. Since she looks exactly like Kitana no one questioned the veil she was wearing over her face, so she was easily able to order the army into a perceived trap...a battle with the Tarkata which they won! Mileena was shocked that she won, but then she realized that she had fulfilled her destiny, the purpose of which she was created by Shang Tsung and Shao Kahn so many years ago: to replace Kitana.
She realized what power she had now, and knew that Baraka, knowing her secret, could pose a danger since she now had decided to assume the role of Kitana. Having his Tarkatan forces slain and knowing Mileena to be a traitor, Baraka sends one of his men to kill Mileena in the Beetle Lair, but he fails. Baraka then takes it upon himself to hunt her down personally, after he orders his remaining men to ambush and kill Sub-Zero(links to sub-zero's ending). He corners her in the Beetle Lair and surprises her...she had thought that the Tarkata sent to kill her WAS Baraka, but he got the upper hand, surprised her, and killed her.
The order of the endings goes: Mileena - Baraka - Sub-Zero