Mileena was the creation of the Shadow Priests by using the dna of Kitana and another Tarkatan female. Some thought she was a bastard of Shao Kahn, Kitana thought that she was the real daughter of Shao Kahn and Sindel.
Mileena had lived a harsh life, being humiliated and despised by everyone. But after Shao Kahn decided to openly invade the Earthrealm, Shang Tsung and the Shadow Priests helped Mileena to claim the throne for herself.
Mileena was the empress, but in fact it was Shang Tsung who ruled it.