Nicaea, a dead face delivery website, reveals to its users a video of their friends' deaths. Most people sign up on the site for trivial reasons, including Io Nitta, Daichi Shijima, and Hiro Kageyama. As they return home from a mock entrance exam, the three students receive a message simultaneously from Nicaea, depicting their gruesome fate in the subway station. Despite being shaken by the email's contents, the trio disregards it until a subsequent earthquake and train derailment causes the premonition to come true.

Swallowed by darkness, Io is posed with a simple question: does she want to die, or would she rather live? Presenting a will to live, Io wakes up in the rubble alongside Hiro, Daichi, and mysterious entities who ask the three of them to "manage" them properly. Soon, they find themselves in the custody of JP's—a mysterious defense force that only operates during a national state of emergency.

After making contact with the otherworldly beings that attacked them earlier, the three students learn that they are now "devil summoners." The Earth is under attack by "Septentriones," strange creatures hellbent on destroying humanity. With their fates now intertwined, Io, Daichi, and Hiro must work together to protect what remains of their planet before being completely obliterated.

Devil Survivor 2: Show Your Free Will is a manga adaptation of the 2011 Nintendo DS video game Shin Megami Tensei: Devil Survivor 2.