The Phantom Thieves are a mysterious group who claim to steal the hearts of corrupt individuals in order to achieve world reformation. Allegedly, those who have their hearts stolen will confess to their crimes of their own free will. However, some people believe that the Phantom Thieves are merely an urban legend.

Ren Amamiya and Ann Takamaki are two members of the Phantom Thieves who learn that Ann's coworker, the glamorous model Mika, is being harassed. Before they can convince her to ask for help by posting on the Phantom Aficionado website, all three witness a top production company executive's medical emergency—an incident that is later theorized to be attempted murder. The rest of the Phantom Thieves agree to investigate the presumed poisoning so they can clear the suspicion aimed at Mika. Soon enough, they find themselves looking into several other matters concerning Ren's "Confidants" from different walks of life and different parts of the city. The pressing question is: could all of the Phantom Thieves' self-proclaimed "missions" possibly be related?