Naoto Shirogane is called on by Touko Aoi, a detective she's idolized for years, concerning the disappearance of two high school students in the city of Yagokoro. Shortly after arriving at their police department, she gets caught up in the rampage of a defective Anti-Shadow Suppression Weapon known as Genesis. This near-death experience gives Naoto's Persona a new form, Amatsu-Mikaboshi. When she regains consciousness, she is told that Genesis - who insists on going by the name Sousei Kurogami - will be her partner for the investigation.
Going undercover at Yagokoro's high school, it's not long until Naoto learns that the missing students are connected to something bigger: a mysterious online poll known as the Midnight Site, where users publicly post information concerning victims of Malicious Slander. Shortly after one of these unlucky people commits suicide, a high-ranking detective disappears...and that's when the administrators of the Midnight Site begin turning up dead. It's up to Naoto and Sousei to track down the rest and draw their killer out of hiding.
This Light Novel contains examples of:
- Bifauxnen: Naoto is still taken for a boy, even with long hair.
- Bittersweet Ending: Naoto solves the case, and the Midnight Site is no more...but the culprit was her former mentor, who succeeded in killing all but one of the Togakushi Judges, and it's highly likely that she might receive the death penalty or spend the rest of her life behind bars.
- Broken Aesop: In Persona 4 proper, Naoto's character arc revolves around wanting to be taken more seriously as a young girl in a male-dominated career. Here, not only is Naoto's more feminine appearance pointless due to everyone she works with still thinking she's a boy, but she ends up having to debase herself repeatedly (read: they walk in on her showering or see her in a pinup catalog) before her coworkers even accept that she's a girl. The worst part is when her boss lecherously "suggests" that she dress and act more like a girl after seeing her swimsuit photos, i.e. exactly how she was afraid of being treated in the first place. At no point are Naoto's protests against her own objectification listened to, and the story treats them as "cute shyness".
- Broken Pedestal: Touko Aoi, who Naoto viewed as a stalwart enforcer of justice, turns out to be the one behind most of the Kagu-Tsuchi killings.
- Canon Discontinuity: While the book itself was originally officially declared canon by Hashino and Soejima (Hashino had a hand in outlining and designing the story and new characters), Persona 4: Arena Ultimax has as good as retconned the book out of continuity, likely due to its mixed-to-negative reception in Japan, and apparent failure.
- Chickification: In the midst of a subplot about accepting her femininity, Naoto loses both her Persona's combat abilities and the more aggressive parts of her personality.
- Colorful Theme Naming: Kyouhei Hioka and Touko Aoi contain characters that can be read as scarlet/red and blue, respectively. Naoto uses this in part to deduce that the purple wire in the time bomb is the one she mustn't cut. Naoto and Sousei's surnames (Shirogane and Kurogami) also contain the words for white and black, which is the title of one chapter.
- Dark Is Not Evil: Amatsu-Mikaboshi, Naoto's new Persona, is a primordial force of evil that feeds off of negative human emotions in Japanese mythology. It's also a non-combative Persona born from her desire to support her friends like Rise.
- Dirty Old Man: Tetsuma Tsuge, Sousei's handler from Kirijo. He tries to play it off as being For Science!.
- Driven to Suicide: The story opens with a teenage girl jumping in front of a train; she turns out to be Kyouhei Hioka's younger sister, Kaoru, who was featured on the Midnight Site. Naoto later notes that there's a very high mortality rate amongst those on the Midnight Site's "List of Sinners".
- "Eureka!" Moment: Sousei's comment that Kyouhei Hioka is "like a ghost" makes Naoto realize that he might already be dead.
- Green-Eyed Monster: Hits twice for poor Kaoru Hioka. First, one of the Togakushi Judges submits her to the Midnight Site for getting too close to a certain boy. And the one who showed her the site was her only friend, Takizawa, out of a secret desire to see Kaoru's agonized reaction.
- Japanese Honorifics: Naoto finds one clue to Hioka's identity by noticing that his first victim corrected herself to use "-san" on his sister, and concludes that the victim was addressing someone they saw as a social superior.
- Knight Templar: The Togakushi Judges believe, to varying degrees, that they have a responsibility to deal with criminals in place of an inefficient police force.
- Knight Templar Big Brother: When gossip drives his little sister to kill herself, Kyouhei Hioka sets out with a powerful handgun and a time bomb to exact revenge; he empties an entire magazine into his first victim, who is another high school student.
- Malicious Slander: What the Midnight Site runs on. Whether it's true or not, more than half of the users voting 'guilty' on any given charge plasters it up there permanently. And yes, some of the administrators have used this to ruin the lives of people they don't like.
- Posthumous Character: Kyouhei Hioka, who was fatally shot after the first Kagu-Tsuchi killing. He's only ever heard through Sousei's Persona ability.
- Rapunzel Hair: Naoto is sporting this now (some pretty dramatic hair growth in just one year).
- Religious and Mythological Theme Naming: The five administrators of the Midnight Site are known as the Togakushi Judges. Togakushi is a famous shrine related to the tale of Amaterasu hiding herself away and plunging the world into darkness, tying into their claims that they shed light on hidden sins. Each of their individual usernames also come from a Japanese deity, usually with some link to Amaterasu. Their killer takes on the handle Kagu-Tsuchi, after the fire god who killed Izanami in childbirth and is generally associated with death.
- Seers: Touko's Persona, Kushinada-hime, can see ten minutes into the future.
- Super Empowering: Amatsu-Mikaboshi's skill, Ability Tune, is a Type 3. It allows Naoto to alter the strength and range of another Persona's abilities.
- Teens Are Monsters: The students of Yagokoro High School have no problem voting people onto the Midnight Site's Hall of Fame for relatively petty 'offenses' (which might not even be true), even though most people featured there end up committing suicide. Two of them are Togakushi Judges.
- Telepathy: Sousei's Persona ability allows him to hear the voices of dead people.
- Vigilante Man: The few Togakushi Judges who aren't using the Midnight Site to indulge their own vendettas are the bad type. Kyouhei Hioka and Touko Aoi start out as somewhat good, but quickly sink to their level.
- Wire Dilemma: The time bomb in the finale has eleven colored wires, one of which has to be left uncut. If the other ten aren't cut in an exact order, it'll go off.