The year is 20XX. The ninja, who once forged the history of Japan, were scattered across the country during the Meiji Restoration. As these ninja mingled with the other clans, their bloodline thinned, and they gradually faded from sight. The descendants of these ninja clans, seeking to preserve their heritage, formed the WNA (World Ninja Association) in the hope of carrying on their legacy. And so it was that the WNA succeeded in developing Ninja-Gum, an art which could summon forth the strength of the Shinobi. And yet creating the most powerful Ninja-Gum requires the strongest of ninja DNA. So it was that the Ninjala Tournament was held, that the mightiest of all ninjas could be found...

1. Final Flight of the Osiris The crew of the Osiris discover an army preparing to invade Zion. While one crew member races inside the Matrix to get the message to Zion, the others try desperately to buy her enough time while fighting off an onslaught of Sentinels they can't possibly defeat. 2-3. The Second Renaissance Part 1 and 2 Humans have created the ultimate AI, which is just as smart as they are. But complications arise when these robots and the humans try to exist peacefully, and eventually all-out war breaks out. The humans ultimately lose the war, and become trapped in the Matrix as seen in the live-action films. 4. Kid's Story A young man discovers that his world isn't real, that it's a computer-generated fantasy land created by robots using humans for energy. He escapes with the help of the hacker Neo. Based on the Matrix trilogy. 5. Program Cis and Duo engage in battle in a virtual recreation of Feudal Japan. 6. World Record While running the fastest race in his life, a champion track star breaks free of his computer-generated world for a small period of time. When he goes back to the real world, he has no memories and is placed in a nursing home. Based on the Matrix trilogy. 7. Beyond While looking for her lost pet, a young woman meets up with some kids in Tokyo to play in a "haunted house," which is really a glitch in their computer world. Based on the Matrix trilogy. 8. Detective Story A detective named Ash is called upon by a mysterious organization to hunt down the notorious hacker Trinity. 9. Matriculated A group of scientists capture a robot and place it in a surreal fantasy world. When the robot's friends come in and kill most of the scientists; however, the robot and the last scientist remaining face isolation in the computer-generated world. Based on the Matrix trilogy.

The Animatrix is a collection of several animated short films, detailing the backstory of the "Matrix" universe, and the original war between man and machines which led to the creation of the Matrix.

In front of a camera, roommates Mao Tsuchiya and Hisashi Ootomo make three promises: Mao must not tell anyone Hisashi is gay and in a relationship with another man; Hisashi must never fall in love or make any advances on Mao; and one must not disturb the other's "personal time." Thus begins their second year of cohabitation. However, everything starts to crumble when the film club—of which Mao is a member—wants to cast Hisashi in the lead role for their upcoming movie. The problem arises with the movie's plot, as it is about boys' love—a romance between a delinquent and the class president. Mao is adamant to dissuade Hisashi from becoming the protagonist due to their first promise; but, to his surprise, Hisashi is easily convinced by the director. After imagining Hisashi as the delinquent he is playing, Mao becomes overly conscious of his presence. He knows Hisashi is just a friend and out of his reach, but Mao cannot keep lying to himself anymore—his feelings toward his roommate may no longer be purely platonic.