After breaking the law of reanimating human corpses, young Watson has to either work for the government or face punishment. He has to go on a secret mission, to find the notes of Viktor Frankenstein, who reanimated the first human corpse.
A 15-year-old boy and 27-year-old woman find an unlikely friendship one rainy day in the Shinjuku Gyoen National Garden. These two broken pieces come together and heal one another as they learn what it is to walk.
After the events of the anime, Rintarou begins to feel the repercussions of extensive time travel, and eventually completely fades from reality. Kurisu, being the only companion to remember him, now must find a way to bring him back.