The Alien Queen is a gigantic three-breasted monster that is encountered in the Duke Dome. She was unleashed on the Duke Dome by the aliens, some time during the start of their invasion (according to the construction workers near the Dome). She quickly made the place her nest, creating the Hive. The Alien Queen is another alien-human hybrid like the first Alien Queen killed in Duke Nukem 3D. Her head is very similar to the Cycloid Emperor, her lower body, which stretches through and out the Hive, is that of an Octabrain. Her breasts and fingers on the claws are that of human. It is notable that she apparently has the same energy inside of her body as the Octabrains: upon being killed, it erupts in an explosion. It appears that the Alien Queen is bred to be a quick way to establish a hive, as she was able to create it in about 4-6 hours. Alien Queen is the mother of the Pregnators and the source of all organic alien lifeforms of the Hive.
She attacks by shooting energy blasts, trying to smash Duke with her hands, or by shooting pods from which Pregnators hatch. Towards the end of the battle, she will call Octabrains that deflect projectiles Duke throws/shoots at her. During 3\4 of the battle, she will protect herself with arms, so Duke has to use pipebombs to stun her. In her final minutes, she become much more aggressive and will stop protecting herself. Upon being defeated, Duke makes the mortally wounded Queen bite her own tongue, after which the energy explodes inside of her, severing the Queen's head.