The events of The Answer begin on March 31, shortly after the end of the original game. During the opening sequence, it is revealed that the Protagonist has died; the other characters speculate that his death is related to his defeating Nyx. The school year has ended, and the dorm is to be closed down soon. Aigis reveals to the group that she will not be attending school next year. During their last dinner party, the SEES members discover that they are trapped in their dorm, and that the day March 31 is repeating itself. Later, a large door-like hole opens in the floor of the dorm, and SEES is attacked by Metis, an anti-shadow weapon similar to Aigis. In the midst of fighting Metis to protect her friends, Aigis's Persona, Athena, transforms into Orpheus, the original Persona of the Protagonist. She also gains the Protagonist's Wild Card ability. Aigis is able to subdue Metis, whose actions were an attempt to end the time skip and save Aigis, who she calls her "sister".
Underneath the dorm is the Abyss of Time, the cause of the time skip. The Abyss contains seven doors, the insides of which contain multi-floor dungeons, similar in design to Tartarus; it is in these areas that the game's combat takes place. At the top of each dungeon, the characters witness an event from the past of a member of SEES. After seeing several of these flashbacks, the characters discern that the event shown in each door relates to how that person had awakened to their Persona. At the top of the seventh and final door, SEES fights a Shadow-like version of the Protagonist. After defeating it, each of them obtain a key. By combining the keys, they would be able to end the time skip and leave the dorm. However, Metis presents SEES with an alternative: instead of unlocking the front door of the dorm, they may also use the keys to travel back in time, to before the fight against Nyx and the death of the Protagonist. Now unable to agree on how to use the keys, the characters determine that they must fight each other to decide. Aigis, Fuuka and Metis claim all eight keys, which fuse into the Final Key. After debating on what to do now, they discover a third, new door in the Abyss of Time, which the group uses (without the Final Key) to travel to the moment the Protagonist sealed Nyx from the world.
Metis explains that the purpose of the seal created by the Protagonist was not to seal away Nyx herself (who is not inherently evil), but to prevent humanity's despair from calling out to Nyx and bringing about the Fall once more. The subconscious will of mankind to despair and wish for death constantly rebirths a monster called Erebus that summons Nyx to destroy the world; Metis implies that Erebus's contact with Nyx is what caused the Fall (that was prevented by SEES). SEES realizes that the wishes that created Erebus also came from them, and so they fight it, and are able to defeat it. Mitsuru points out that Erebus will return, as humans will never stop wishing for death. After breaking the time skip and exiting through the front door of the dorm with the Final Key, Metis, Aigis, and the rest of SEES are summoned to the Velvet Room, much to Igor's (pleasant) surprise. It is here they learn of Metis's true origins: that she is a manifestation of a part of Aigis's personality. Distraught over the death of the Protagonist, she no longer wanted to live like a human, and wished to return to being a machine. However, after being set free from the Abyss of Time, Aigis changes her mind, deciding to continue to attend school, something she had chosen not to do earlier.
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