Kouichi Hayase is a high school student who is often bullied at school, but dreams of one day becoming a hero. After being bullied into buying stuff for his schoolmates, he decides to take a shortcut through a forest, which is when a giant object falls on him. After regaining consciousness, he sees a giant robot in front him and a naked girl lying beside him. He covers her with his jacket, and after waking, she is revealed to have partial amnesia and goes with him to his house. Soon after, other giant robots begins to attack the town. The girl tells Kouichi that they are enemies, and goes into town with the intent of fighting them. Following her, Kouichi encounters his friend, Hideaki Yajima, who plans to use himself as bait in order for the two to get away. After Kouichi reveals his frustration in not being able to do anything, the girl reveals her name, Emi Kizaki, and has him summon a giant robot (Machina) called Linebarrel. Though he defeats the enemies with his newfound power, he is shocked when Emi tells him that he is dead.
At an unknown location, the Kato-Kitan Corps, which belongs to an organization bent on capturing the Machina Linebarrel, and JUDA, which is publicly known for being the world's largest medical equipment maker, are engaged in a heated battle. With JUDA's forces being overpowered, they ask for reinforcements, which comes in the form of another Machina called Vardant and its pilot, Reiji Moritsugu. As he handles the enemy, the other members of JUDA are discussing the recent actions of their enemy, the Katou Organization. Meanwhile, Kouichi's family welcomes Emi into their household, and Kouichi shows his newfound abilities and confidence at school by beating those who bullied him. Later, Kouichi expresses his gratitude to Emi for having killed him, giving him a new life, after which the Kato-Kitan begins a new attack to lure out the Linebarrel. Kouichi is thrown into battle once again, and two of JUDA's Machinas are also in the fray in an effort to stop the enemy as well. Kouichi, however, declares that he is the only real "justice", and goes on to fight both sides, not realizing the collateral damage he is causing. After the Machinas retreat and Kouichi declares his job done, Emi and Yajima are stunned to see his actions and the damage he has caused.
After failing twice to deal with Kouichi, JUDA sends their best pilot, Reiji Moritsugu, to the task. Meanwhile, Kouichi's friend, Hideaki Yajima, is getting even more worried about his arrogant and aggressive behavior.