Persona 3 is a departure from its predecessors in that the story moves at a prescribed pace from day to day over the span of a calendar year, rather than jumping from one narrative event to another in typical console role-playing game fashion. Like in previous installments, the main character attends high school; however, in this game school activities are important in building up the Main Character's attributes. For example, studying in the library builds "Academics," drinking "Pheromone Coffee" builds "Charm", and singing Karaoke builds "Courage". Creating "Social Links" by building relationships with classmates and acquaintances is of particular importance, as the strength of each link will eventually affect the strength of the Main Character's performance in battle. This "day in the life" style of gameplay is similar to Japanese console RPGs with dating sim elements, like Harvest Moon, Azure Dreams, or Atlus' own Imodoki no Vampire: Bloody Bride.
While half of the game is dedicated to participating in a typical teenager's life (socializing, attending clubs, studying, etc.), the other half involves roguelike dungeon-crawling in Tartarus, the monster-infested labyrinthine tower that your high school transforms into at the stroke of midnight. Every few floors features a boss battle and chests full of money and items are randomly strewn throughout. The floors do not have set maps, except for the small boss floors, and are randomized each time the player visits.
The battle system is a turn-based affair, with the Main Character and his comrades using their Personas to exchange blows with their enemies. Persona 3's battles also feature a system dubbed Once More, similar to the Press Turn battle system used in other recent Shin Megami Tensei games such as Digital Devil Saga, in which the player is rewarded for exploiting enemies' elemental weaknesses. However, instead of rewarding the entire party, extra turns are given on an individual basis. If a player attacks a Shadow weak to fire with fire, it is knocked down. If all enemies are knocked down, an "All-out Attack" can be performed, where all party members rush the enemies at once, dealing massive damage in a large dust cloud as comic-book style onomatopoeia ("Bam!") appear above.
Only the protagonist is directly controllable in battle, while the numerous allies that join the party are governed by AI. The player can give the AI guidelines using preset "Tactics" like "Heal/Support" or "Full Assault", more of which are accumulated over the course of the game. These AI allies and the main character himself are subject to a physical well-being parameter which moves from "great" to "good" to "tired" or "sick" over the course of exploring Tartarus. If a player or friendly NPC is "tired" or "sick", their performance in battle drops dramatically, and is more likely to take a critical hit. Also, if one character is sick, they may also pass on the illness to other characters. Resting a night or two can restore the character's health.
In combat, the Main Character and his allies summon their Personas using a pistol-shaped device called an "Evoker" by aiming at their heads and pulling the trigger. With the aid of their Personas, the party is able to cast spells and perform special attacks (characters can also perform basic physical attacks themselves). While your allies in the game can only bring forth one Persona, the Main Character is able to gain many Personas and even change them in battle. When Personas level the player inherits its natural attributes in the form of basic stats such as strength and magic. New Personas can be acquired via a post-battle shuffle card game, or through fusion of two or more existing Persona. Here the social sim aspect of the game meets the dungeon hack portion, as the amount of bonus experience granted to a given Persona being created is determined by the strength of the Social Link with which that Persona's "Arcana" corresponds. Low-level Social Links will grant small bonuses, while higher levels give generous portions. Maxed out Social Links are required to create the most powerful Persona in each particular Arcana.
The Main Character is a teenager who was orphaned as a young boy that returns to the city of his childhood. Shortly after transferring to Gekkoukan High School, he is attacked by Shadows—-creatures that feed on the minds of their victims. The assault awakens his Persona, Orpheus, his only chance at defeating these creatures of the night. He soon discovers that he shares this special ability with other students at his new school; each is armed with an Evoker, a special handgun that they fire at their heads that does not harm them physically but causes emotional stress in order to summon forth their own Persona. The Main Character learns that he is unique among the other members, being able to use multiple Personas and that he is guided by the formation of Social Links to improve his power. From them he learns of the "Dark Hour," a hidden time that exists between one day and the next, swarming with Shadows. He joins the Specialized Extracurricular Execution Squad (SEES), and with his new friends, confronts the threat of the Shadows by exploring Tartarus, a huge, chaotic tower that appears in the place of their school every Dark Hour.
After signing a contract in which he "accepts his fate of his own free will," the Main Character battles with the other members of SEES against the Greater Shadows, incarnations with traits and appearances similar to those of the first twelve Major Arcana of the Tarot. The group is told by Shuji Ikutsuki, the adult supervisor of the group, that defeating all the major Shadows will end the Dark Hour. The Main Character continues to encounter and eventually befriends the child-like entity that appears only during the Dark Hour who refers to himself as Pharos, and who is really the incarnation of Death, the thirteenth Arcana. SEES also encounters members of Strega, people that also are aware of the Dark Hour and have their own Personas, but instead of fighting the Shadows, use the time and their abilities to perform illegal activities including assassinations. Once Strega learns that SEES is trying to stop the Dark Hour, they attempt to prevent SEES from succeeding but fail, two of the members, Takaya and Jin, appear to commit suicide realizing they cannot stop SEES' goals.
After SEES destroys the twelfth Greater Shadow, the group finds that the Dark Hour and Tartarus still occurs and they were being used. It is revealed over the course of the game that an event ten years prior are the cause of the Shadows; an experiment at the Kirijo Corporation laboratories was designed to collect Shadows in order to bring about the end of the world. However, the experiment failed, and released Nyx prematurely, as well as creating the Dark Hour and Tartarus. Aigis, a powerful robot designed as an anti-Shadow weapon, was sent to destroy Nyx but was unable to do so, instead she was only able to disperse twelve Greater Shadows from the main body, and installed the last in a young boy that happened to be nearby - that being the Main Character. The Kirijo Corporation covered up the incident by rebuilding the local area, including Gekkoukan High School. Shuji Ikutsuki, a former researcher for Kirijo, used the members of SEES to destroy the Greater Shadows, because of this the Shadows were able to meld back into the single being, allowing Death to emerge in the form of Ryoji Mochizuki, the teenage version of Pharos.
After SEES befriends Ryoji, he reveals that his time spent with the main character has changed him from the creature he once was, and tells them that they must kill him. If he remains alive, then on January 31st- against his will- he will usher in Nyx, the harbinger of Death. At this point, the player may opt to kill Ryoji, which delays the end of the world and erases the memories of the last year, allowing SEES to live normal, peaceful lives until the inevitable. Alternatively, if the player opts to leave Ryoji alive, then the game continues to January 31; during the Dark Hour, SEES climbs to the top of Tartarus, encountering and defeating Takaya and Jin en route, and eventually battle with Ryoji, who has become an avatar of Nyx. However, despite being defeated, Nyx Avatar rises up into the sky, causing the moon to crack open and revealing a strange device that begins to kill people across Earth. The Main Character uses all of his Social Links to complete his true arcana--the 21st arcana, "The World"--and is able to use its power to seal Nyx away. The memories of the past year are erased as the world returns to normal.
The members of SEES attend their graduation ceremony but, despite the loss of memories, are aware they share a connection and that they promised to gather on the school's roof should they make it to graduation day. There, they find Aegis with the Main Character laying in her lap; as further described in Persona 3: FES, the Main Character, though having physically survived the battle with Nyx, is forced to sacrifice his soul to keep Nyx sealed away forever, and falls into a coma after the brief reunion. The story is continued in Persona 3: FES' "Episode Aegis" expansion/sequel, which revolves around Aigis' inability to accept the Main Character's fate, nor its necessity after Nyx was unleashed, and the results of her conflict with the Main Character's sacrifice.