Plot summary
In the mid 21st century, in the midst of a snowstorm in summer amid a ruined city, the protagonist fends off ethereal black monsters to protect a sick young girl named Yonah. The protagonist uses a magical book to fend off the creatures, but Yonah touches it and is covered in black markings, worsening her condition. The story moves to over a thousand years later, with the current feudal civilization in decline and the black creatures—dubbed Shades—becoming more hostile. The protagonist and Yonah live in a village built within post-industrial ruins, with the protagonist taking odd jobs from the village leaders, twin sisters Devola and Popola, to earn money to support the sick Yonah.
While rescuing Yonah from a temple after she wanders there looking for a rare flower, the protagonist meets the talking book Grimoire Weiss, which suggests that the two team up to use Weiss's magic and to find a cure for Yonah's disease, identified as the terminal Black Scrawl. In their search, they encounter Kainé, a hot-tempered and foul-mouthed swordswoman, and Emil, a blindfolded boy whose eyes petrify anyone they see. After journeying for a time, the protagonist's village is attacked by a giant Shade. The battle ends with Emil being forced to petrify Kainé to seal the shade, and Yonah being kidnapped by a master Shade dubbed the Shadowlord.
The game jumps forward five years, with the situation worsening. The protagonist and Emil successfully find the power necessary to free Kainé and kill the giant Shade, but getting the power transforms Emil into a skeletal being the villagers fear. Under Devola's and Popola's guidance, the party seeks parts of a stone key that will unlock a pathway to the Shadowlord. After defeating five Shades and assembling the key, the team goes to defeat the Shadowlord. Devola and Popola then confront the party, revealing themselves to be allied with the Shadowlord in the name of a greater plan. 1300 years prior, humanity faced extinction due to an incurable disease.
In an attempt to survive, they separated their souls from their bodies; the current humans are artificial Replicant bodies who developed their own personalities, while the Shades are human souls—dubbed Gestalts—who are slowly losing their minds through being unable to reunite with their bodies. The Black Scrawl is a side effect of the Gestalts' insanity degrading their Replicant counterparts. The Shadowlord is the prime Gestalt used to stabilize them, and Devola and Popola are androids who oversee the system. The party defeats the twins, with Emil sacrificing himself in the process.
The remaining group then defeats the Shadowlord, revealed to be the Gestalt of the prologue's protagonist, with his actions driven by the wish to save his Yonah by reuniting her Gestalt and Replicant. Though successfully rejoined, the Gestalt Yonah dissipates to save her Replicant version's life, and after Grimoire Weiss sacrifices himself to weaken the Shadowlord's power, the protagonist kills him.
If the player enters further playthroughs, events start just after Kainé is freed. Kainé's past is focused on, showing the discrimination she suffered due to her parents' deaths, being born intersex, and later being partially possessed by the rogue Gestalt Tyrann. Through Tyrann, the player can understand the previously garbled speech of Gestalts. New story sequences show the Gestalt antagonists' motivations and backstory, showing them to be sentient and fighting for their own beliefs and goals. The second ending shows the spirit of the Gestalt protagonist and Yonah reuniting in the afterlife and reveals that Emil survived; further information confirms that the Shadowlord's death will lead to humanity's extinction as Replicants and Gestalts can no longer be rejoined.
In a third or further playthrough, Kainé becomes overwhelmed by Tyrann, going berserk and forcing the protagonist to fight her. The protagonist can either kill her to end her suffering (the third ending) or sacrifice his life for her (the fourth ending). The latter choice erases memory of him from Kainé and Yonah and deletes all of the player's save data.
The updated version of Replicant adds a fifth ending after a new game is begun following the fourth ending, beginning after the defeat of Kainé's Shade nemesis Hook. Three years after the Shadowlord's defeat, Kainé continues having nightmares about losing something precious and fights increasingly hostile Shades. Investigating a settlement, she finds its people killed by robots emerging from its central tree, the control unit recording Replicant memories. Kainé is talked to by the control unit's AI through twin childlike avatars. She is aided in battling machine duplicates of her by Emil, eventually entering the tree's mainframe and battling enemies drawn from her memories. She ultimately battles a more powerful Hook, helped by the data remains of Grimoire Weiss. Kainé destroys Hook and the AI, restoring the protagonist in his young form; all of the player's save data prior to the fourth ending is consequently restored.
Credits
Adapted from Wikipedia contributors, Nier (video game). Section headings and formatting adjusted.