Ajin is a live-action adaptation of a Japanese manga series written and illustrated by Gamon Sakurai. Kei Nagai dies in a car accident, but realises he is a type of immortal known as Ajin (demi-human). Hunted by humans, Ajin is eventually found by the government and used as a subject in cruel experiments. He finds fellow demi-humans along the way as he escapes and goes on the run.

The story centers around female high school student Setoka Tachibana, who has confessed her feelings to other boys 12 times, but has been rejected each time. Her older brother Haruka Tachibana cares for his younger sister deeply, but keeps a secret from her that they are not blood related. One day, Setoka's first love Takane Serikawa appears after many years and approaches her.

When she was a middle school student, Futaba Yoshioka liked Kou Tanaka who was unlike the other boys and quite gentle. Kou Tanaka then moved away and they lost contact. At the end of Futaba Yoshioka's first year as a high school student she meets Kou Tanaka again. Kou Tanaka’s name has changed to Kou Mabuchi and his personality seems different from his middle school days.

Residents in a town have a hard time due to the land tax and forced labor. 9 people, including Juzaburo Kokutaya (Sadao Abe), worry about the future of their town. They then set up a plan to save the town. The plan is to lend large amounts of money to han (historical term for the estate of a warrior) and distribute the interest annually to the residents, but if they're caught they will lose their lives.

Yu Akahane (Nana Komatsu) moves to a dormitory room after her father's transfer from work. She is excited that she will live in the same dorm as Takumi Shirakawa (Yudai Chiba) aka "White Prince." Yet, Haruto Kurosaki (Kento Nakajima) aka "Black Devil" kisses her as punishment for going against him. It is Yu Akahane’s first kiss. Since then, she becomes obedient to Haruto Kurosaki.

A temporary worker at a company gets involved in a big case when her boyfriend leaves his smartphone in a taxi.

Teiichi Akaba is a student at a prestigious private male high school known for producing important politicians and bureaucrats. His dream is to become the prime minster and make his own country. To help achieve his dream, he wants to become elected as his school's student council president. The elected student president receives privileges and a better chance for promotions later in the political & bureaucrat world. A power struggle takes place surrounding the student election.

Arata Kaizaki is 27-years-old and unemployed. He quit his prior job after working for the company for 3 months. Arata Kaizaki decides to take part in a research program. He takes medication that makes him look younger and he is to attend high school for a year. There, he falls in love with female high school student Chizuru Hishiro.

In 1868, a battle between new government forces and shogunate forces are about to take place in Edo. Katsu Kaishu (Hiroshi Tamaki) wants to avoid useless bloodshed and sends a peace envoy to Takamori Saigō, but Katsu Kaishu is unable to get a response from Takamori Saigō. One day, Katsu Kaishu meets high school teacher Mikako (Satomi Ishihara) and her student Masaya who is captivated by the shogunate. Mikako and her student Masaya tells Katsu Kaishu that they are from the future. Katsu Kaishu takes care of Mikako and her student Masaya, while Mikako hopes to go back to the future where she came from.