For the sake of convenience, the protagonist will be referred to by his canon name from Persona 3: The Movie: Makoto Yuki.
This page contains unmarked spoilers. Read at your own risk.
When the clock strikes twelve, the world around Makoto changes: people around him disappear into coffins, electronics stop working, the streets become caked in blood, and the sky turns an alien shade of green as the moon gives off a bright golden glow. For Makoto, however, this is nothing unusual...
He makes his way to the dormitory for the school he would be transferring to this year, Gekkokan High. When he arrives, he is greeted by a young boy in striped clothes, presenting him a "contract" that states he would take responsibility for his actions over the coming year.
Makoto signs the contract, and the boy cautions him about how time would deliver all to the same end before vanishing...
After the boy vanishes, a young girl appears. She appears to be apprehensive, and begins to reach for what appears to be a gun in a thigh-strapped holster. She is stopped by an older girl, who stays her hand until the lights in the dormitory come on and the world around them returns to normal.
The older girl introduces herself as Mitsuru Kirijo, a senior at Gekkokan and student council president. She also introduces the girl who was about to draw a gun: Yukari Takeba, a fellow junior. Mitsuru has Yukari show Makoto to his dorm.
That night, as Makoto sleeps, he has a dream where he finds himself in a large and lavish elevator. He is greeted by the long-nosed man present, Igor, master of the Velvet Room, who, along with his assistant Elizabeth, would become a fixture of his life for the year to come.
The next day, Makoto arrives at Gekkokan. He winds up in the same class as Yukari, as well as an old acquaintance of Yukari's: Junpei Iori, a classmate who knew Yukari since the previous grade.
On the night of April 9th, while Makoto slept, chaos erupts around the dormitory. Akihiko Sanada, the boxing team captain and another senior, comes into the dorm, his arm injured, warning Mitsuru and Yukari that something big was coming. Mitsuru instructs Yukari to get Makoto and take him to safety.
Yukari guides Makoto to the rooftop, but the two find themselves cornered by a bizarre monster that Yukari calls a "Shadow". Yukari reaches for her gun and, strangely, points it at her own head. Before she can pull the trigger, she is knocked aside by the Shadow.
Makoto moves to aid her, but stops when he sees the gun on the ground. He picks it up and, compelled by a mysterious force, points it at his head. He hesitates for a few moments, but then grins and whispers...
Makoto pulls the trigger, and from the explosion of energy bursting from the other side of his head appears his Persona: Orpheus. Makoto uses Orpheus to attack the Shadow, but for a moment, loses control of his power, causing Orpheus to transform into another, more monstrous Persona which tears the Shadow to shreds before changing back into Orpheus, with whom Makoto finishes off the stragglers before passing out.
Makoto dreams once more of Igor and the Velvet Room. Igor congratulates Makoto for awakening his Persona, and describes his power as being like the number "zero": empty, but with limitless potential, allowing him to use multiple Personas. Igor advises Makoto to forge and cultivate bonds with the people in his life to strengthen his potential.
Makoto awakens in the hospital a week later, with Yukari waiting for his recovery. Yukari apologizes for keeping secrets from Makoto, and confides in him the fact that the two have more in common than he initially thought: similar to how Makoto's parents died in an explosion in Iwatodai ten years ago, Yukari lost her father around the same time.
All of the students in the dorm, including Mitsuru, Yukari, and Junpei, along with Ikutsuki, are members of the "Special Extracurricular Execution Squad", or SEES, a special organization dedicated to investigating the cause behind the Dark Hour and the appearance of Shadows. All members of SEES, save for Ikutsuki, possess the ability to summon a Persona through the use of a special device, the gun-shaped "Evoker". As such, Ikutsuki and Mitsuru invite Makoto to lend his strength, an offer Makoto readily accepts.
At the core of the Dark Hour and the Shadow outbreak is Tartarus, a bizarre tower that emerges from beneath the school during the Dark Hour. With Mitsuru providing logistical support, Makoto leads Yukari and Junpei, who possess their own Personas in the forms of Io and Hermes, into the tower, fighting Shadows while gradually making their way to the top of the tower and maintaining their scholarly and civilian lives during the day.
On May 9, the night of the full moon, a large Shadow suddenly appears at the Iwatodai rail station. Makoto, Yukari, and Junpei go to investigate, eventually finding themselves trapped in a monorail car that had been commandered by the large Shadow, the Priestess. Thankfully, the Priestess is destroyed, and the monorail is halted before an accident could be caused.
On May 9, the night of the full moon, SEES commence a mission to rescue Fuuka from Tartarus. Shortly after finding Fuuka hail and whole, the team is recalled to the tower's entrance as two large Shadows, the Emperor and the Empress, attack Mitsuru and Akihiko. Natsuki, the same bully that had caused Fuuka to be trapped in Tartarus, wanders into the tower, driving Fuuka to take a nearby Evoker and summon her own Persona, Lucia. With Lucia, Fuuka is able to uncover the weaknesses in the Shadows, helping Makoto and company destroy them.
Natsuki, remorseful over having endangered Fuuka's life, apologizes profusely before she is taken from the tower. The following day, her memories of being in Tartarus are gone, but her personality has changed radically as she offers a hand of friendship to Fuuka.