In an effort to learn more about the metallic aliens that have been plaguing the planet for the past years, Dr. Noguchi and his assistant Maki Agata try to bring to life a construct pieced together from the destroyed aliens.
They recruit Takuto Kaneshiro, Maki's boyfriend at the college they both attend, into this project because of his talent for metallurgy. While Takuto is unhappy with Maki keeping secrets from him again, he reluctantly helps with the project. However, in the process of reviving the monster that Dr Noguchi has aptly called Frank (short for Frankenstein), unidentified soldiers invade the MORGUE facility. They cut the power, leading to a power surge which violently brings Frank to life and causes an explosion that kills everyone in the facility except Takuto.
"Mr. X" visits the scarred (emotionally and physically) Takuto in the hospital, and offers him a chance to get his vengeance on the monster he blames for killing Maki and destroying his life. Months later Lt. Ryu Soma is reborn from the ashes of Takuto's soul, as a military pilot who joins FUNERAL. This is the organization which deals with the attacking aliens, and has also recaptured Frank (who escaped after the explosion at MORGUE).
It quickly becomes clear that Frank has become the best weapon FUNERAL has to defend against the aliens, which leaves Ryu torn between revenge and the desire to protect his comrades. Further complicating the picture, the only person who can communicate with Frank is a young girl named Hattie, who bears a striking resemblance to Ryu/Takuto's lost love Maki. As it becomes apparent that Frank is more than a simple monster, Ryu and his FUNERAL comrades have to come to terms with questions of human identity, grief, and loss.