The story drags us into the daily life of Mashiro, a handywoman, who takes care of helping the people of the village. One day, the Dominantor Empire invades the region and captures all the women to make them their slaves. When her friend dies before her eyes, Mashiro, mad with anger, manages to wake up the millennial robot who was secretly residing in the village. It is now her chance to stop the thirst for uncontrollable power of the Dominator Empire. Soon, she is joined by other mecha pilots in this crazy quest to oppose an entire Empire.

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.