First appearing in Mortal Kombat II, Mileena is a clone of of Princess Kitana, created by the sorceror Shang Tsung. When creating her, he used Tarkatan essence, which is the reason for her sharp, Tarkatan teeth hidden underneath her mask. Mileena has a deep hatred for her twin, Kitana. She feels that it her right to rule Edenia as princess.

After Shao Kahn conquered Edenia and merged it with Outworld, he adopted princess Kitana as his daughter. Although loyal to the emperor, Shao Kahn feared that she may one day betray him, should she ever discover her true past. He then ordered Shang Tsung to create a clone of Kitana to take her place as his daughter. Shang used the essence of Kitana, but also used Tarkatan essence to fill in the remaining aspects of his creation. This caused unfavorable results, ending with a perfect representation of Kitana, but with Tarkatan facial features.

However, instead of destroying Mileena as a failed creation, Kahn decided to introduce her as Kitana's twin sister. Her main duty was to make sure the princess remained loyal to him. However, as he feared, Kitana did eventually discover her past. During the events of Mortal Kombat II, growing suspicious of Kitana, Shao Kahn ordered Mileena to watch over Kitana. After learning that Kitana was indeed conspiring with the Earthrealm warriors, Mileena attacked Kitana. However, Kitana proved to be the superior warrior and killed Mileena.

Now damned to the Netherrealm, Mileena was recruited by the fallen elder god Shinnok. During the events of Mortal Kombat 4/Gold, Mileena assisted Shinnok in his invasion of the recently freed Edenia. However, she was once again defeated by Kitana and secretly imprisoned for many years.

When Onaga, the Dragon King, returned during the events of Mortal Kombat: Deception, he too began an invasion of Edenia. Baraka learned of Mileena's whereabouts and freed her from her confines. She joined Onaga and was ordered to pose as Kitana to mislead and confuse the Edenian forces. However, after Onaga's defeat, Mileena decided to seize control of the Edenian armies, completely.

During the events of Mortal Kombat: Armageddon, still under the guise of princess Kitana, Mileena used the Edenian armies to seize Shao Kahn's fortress in Outworld. Now confident that Outworld was hers to rule, she was suprised when Shao Kahn, along with Goro and Shang Tsung, fought their way into the throne room, where she was hiding. When finally face-to-face with Kahn, Mileena revealed her true identity to the emperor and surrendered to him.

Accepting her surrender, Shao Kahn commands Mileena to capture Shujinko to use as a bargaining chip to gain Onaga as an ally. She sends Shujinko a false invitation to meet her at Shao Kahn's fortress. Shujinko is fooled by her trickery, and is quickly imprisoned upon arrival.

However, Mileena is still no longer able to accept being a mere servant. She once again sets her sites on ruling Edenia. She travels to the realm in hopes of gaining godlike power by defeating Blaze.