In 1988, mysterious mechanical living bodies known as Ancient-JINKI appeared from within La Gran Sabana, Venezuela and attacked humanity. In response Japan formed a secret society known as 'Angel' to defend against the attacks.

JINKI tells the story of a 14-year old, robot modelling girl named Tsuzaki Aoba. She encounters a giant JINKI robot type, called the Moribito-2, and ends up joining Angel to fight against the Ancient-JINKI and an unknown force.