Shuu Tsukiyama is a ghoul: a creature who eats human flesh, and he likes to enjoy his meals to the fullest. One night, while relishing in the premeditated murder of his dinner, Shuu's much anticipated first bite is disturbed by a sudden flash of light. The flash turns out to be from the camera of high schooler Chie Hori, who presents Shuu with the perfect picture capturing his true nature; the extremely clear shot of a bloody corpse and an overly excited Shuu threatens to expose his ghoul identity, thus Shuu needs to sort out this situation quickly. After Shuu discovers that Chie attends the same high school as him and is even in the same class, the reason behind his feelings of obsession changes from self-preservation to morbid curiosity. As he grows closer to the absent-minded and extremely odd photographer, he challenges them both to learn more about each other's conflicting worlds; Shuu promises that Chie will come out of this experience with a photograph superior to the one she already has.

The battle against Tendou Kodzunu is over, and the Magami Five begin to look forward to their senior graduation, hopefully planning for their adult futures. However, life in Tokyo is not at peace... The underground assassin group known as the Twelve Heavenly Generals of the Martial Fist begin to move against those protecting the city from demons. Normally rumored to kill criminals that the mundane law was unable to bring to justice, the Martial Fist now set their sights on Tatsuma Hiyuu, Kyouichi Houraiji, Aoi Misato, Komaki Sakurai, Yuuya Daigo, and Hisui Kisaragi. What is the purpose of this cruel turn of events? And who ordered the hit? New threats emerge as others awakened to powers unleashed by the Ryumyaku seek out the Magami kids - and old friends now return as enemies. Destinies will collide as the Stars of Fate begin to merge; Yin and Yang will meet. And soon the shadowy figure pulling the strings will reveal himself, in an effort to raze Tokyo to the ground and awaken the Vessel of the Golden Dragon.

One Christmas Eve, Hana, Gin, and Miyuki are rummaging for presents through heaps of garbage when they chance upon an abandoned baby in the cold winter night. Appalled at the pitiful sight, Hana's maternal instincts kick in and she insists on finding the baby's biological mother to demand an explanation. Naming the baby Kiyoko—meaning pure child—they begin their search using the possible clues left alongside her: a mysterious key and a single note. However, their plans are soon thrown into disarray as they get caught up in a series of unprecedented events. Tokyo Godfathers follows the journey of the trio as they stick together through thick and thin, hoping to deliver Kiyoko to her true home, and find their very own Christmas miracle.

Something evil is stirring in the shadows of Tokyo... During the spring of his senior year in high school, quiet Tatsuma Hiyuu transfers to Magami Academy in Shinjuku. The mysterious boy's outsider status and his profound skills in martial arts quickly earn him the friendship of class delinquent Kyouichi Houraiji. Through an uncanny connection and a happenstance challenge, he also meets Yuuya Daigo of the wrestling club, the captain of the girls' archery club, Komaki Sakurai, and Aoi Misato, the Student Council President. During their encounter, there is a sudden, harsh disruption of the Ryumyaku (literally Dragon Pulse, otherwise known as Dragon Vein or Dragon Stream), the flow of arcane energy. The surge awakens within the five teenagers a latent power, giving them each a supernatural ability. Enlightened to their newly acquired gifts by Hisui, the young heir of the Kisaragi Clan who maintains his family's antiques shop - as well as their duty to protect Tokyo from Oni (demons) - the Magami students decide to use their power to protect the city from the onslaught of dark forces. Battling the demons alongside Hisui Kisaragi, the five unlikely friends discover that they may have to face a greater threat to Tokyo other than destroying a few malevolent, random monsters. The Ryumyaku had been disrupted by force, from someone invoking the Dark Arts - and that person has a wicked desire to unleash a long-dead evil. Can the teenagers overcome their own fears and flaws to fight against the Dark Arts? And soon they will also have to face their own destinies as they discover their Stars of Fate. This anime is based on a manga, which was based on the Nintendo role-playing video game originally released in 1998.