Absolute Duo follows the viewpoint character, Tor, who enrolls in Koryo Academy, a high school where its students battle each other with weapons known as Blaze (焔牙/ブレイズ Bureizu?) as training to become future peacekeepers. The students must pass a battle during the qualification ceremony of the freshmen day in order to be enrolled in the academy. Although most students manifest their Blazes as melee weapons, Tor’s ability manifests as a shield, making him an Irregular (イレギュラー iregyurā?). The school uses a special Duo system in which students are assigned partners. Tor is paired with Julie Sigtuna, a silver-haired beauty fromScandinavia, and must share a room with her. Both Julie and Tor are revealed to be an avenger, while Julie herself is an El-Awaken and possesses unlimited power. They both also have tragic pasts because their loved ones, Tor’s sister and Julie’s father, were killed by an enemy. Tor previously befriended with Imari Nagakura who failed the qualification and is enrolled in the Koryo branch academy on a vacation island and later paired with Miwa to form a duo.
Tor also later get along with other known classmates such as Tomoe Tachibana, Miyabi Hotaka, Aoi Torasaki, and Tatu who also passed the qualification ceremony, principal Sakuya Tsukumo, and an energetic teacher, Rito Tsukimi. One day, a blonde haired beauty named Lilith Bristol heard of Tor’s ability, and transferred from the English Branch Academy in order to pair up with Tor to form a duo without attending classes. She declares her love with Tor but she is rejected. Lilith becomes angry and one day she trespasses a training lesson and challenge the students there. Nevertheless, Lilith still not give up and try to win Tor’s heart. Tor spends his school life with all his classmates and teachers, such as attending lessons, having tea with Lilith and strolling out in shopping malls once in a while.
Tor’s school life used to be all-normal until one day Equipment Smith and K interrupts the normal school lives of the Koryo Academy students because they have the same goal that is, to build a strong force that conquers the world with their co-produced Units. Equipment Smith is revealed to have deep vengeance towards Sakuya’s family for exceeding his research and Lilith’s family for abandoned him to search for another career. When the academy held a summer trip at the island where located one of Koryo academy’s branch school, they sent rebellious forces to attack the students and kidnapped Miyabi, who feels depressed because she is weak to help her friends and wish for greater power. Days later, the forces infiltrated the school compound led by K, Equipment Smith and followed by Miyabi, who is made their slave because of her wish. Tor and his friends united their power defeated K, Tomoe put Miyabi back to normal and all K’s force units are defeated by all the academy’s students. Due to K’s defeat, Equipment Smith insulted K, thus makes K killed the former. The same night, K continued attacking the school the second time all by himself but was later defeated again by Tor and Julie, thus apprehended. The remaining thing unknown is that Sakaki Narukami, who killed Tor’s sister and Julie’s father is quietly moving behind the scenes.