In the graphic novel series of the manga Battle Angel Alita (written by Yukito Kishiro), the Ouroboros Program is a program developed by the mad scientist Desty Nova. Alita is trapped inside the program in the final two books: first, Fallen Angel, and later in Angel's Ascension. Nova states, "Her psyche is trapped inside my Ouroboros Program. She'll wander the labyrinth of her karma--for ETERNITY!!" A footnote in the book explains, "Nova's program--named after the symbol of disintegration and reintegration, the serpent swallowing its own tail--can manipulate Alita's memories and subconscious."

Alita is first transported back to the Scrapyard, where she is forced to fight her old enemy Jashugan in a game of motorball (which is reminiscent of Rollerball). When she defeats Jashugan, thus overcoming her karma, she escapes from the program. The second time, she is transported to a time when she first became a Hunter-Warrior, and is forced to kill her beloved father-figure, Daisuke Ido. She lives through this dream for months, enjoying a happy fabrication of the past, until Kaos Nova invades the dream and fights alongside her.

The Ouroboros is also briefly mentioned in the novella Singularity, a great sci-fi novel about two boys who stumble upon a shed which houses an event horizon, allowing time to move significantly faster than the outside world. A monster eventually obliterates the shed, coming out of the sink and thrashing about as it tries to eat its own tail.