The Lost Verses and the Red Sky had Nier and Yonah fleeing from a Red Eye attack. She was separated from her brother in the panicking crowd of pedestrians and wandered the streets hoping to find him. Kainé found her and brought Yonah to her home for protection. Though their time together is brief, Yonah felt comforted by Kainé's kindness and respectfully called her "Sis."
During the beginning of NieR, she and Nier were hiding in a supermarket from the attacking relapsed Gestalts. After dispatching three of them, Nier checks on Yonah. After reassuring Yonah that he'll protect her, Nier returns to the entrance only to find more shades. Nier fends off three to four shades before being knocked to the ground. Overwhelmed, he decides to give in to the Black Book, trading his soul for power. Nier fights dozens of shades using the book's power, easily killing all of them.
When he hurries back to Yonah, she offers him a cookie. Yonah starts uncontrollably coughing, when a bunch a markings start traveling up her body. She reveals she touched Grimoire Noir to help her father/brother and turned into a Gestalt, already beginning to relapse.
The Lost Verses and the Red Sky adds that she fell into a coma soon after this occurred. Finding a cure for her immobile state was the sole motivation for her brother agreeing to become the Shadowlord. Not even the scientists behind Project Gestalt were able to find a cure for her. Even her brother's power as the Original Gestalt could not cure or help her. It would have been easier for her to die but, to avoid jeopardizing the entire plan with Nier rebelling, her Gestalt was instead placed in a cold sleep. Her Replicant's creation was done to ensure that her soul would have a body to return to after a thousand year wait.
1,412 years later (1,312 in NieR Gestalt) when Nier and his allies come to save Yonah from the Shadowlord, Yonah is seen in a comatose state. The Shadowlord then appears before the group and battles them, nearly losing to Nier.
Yonah then begs for them to stop. As she and Nier walk towards each other, Yonah continues toward the Shadowlord. It is revealed that she is the true Yonah whom the Shadowlord (Gestalt Nier) was trying to prevent from relapsing. She states that she doesn't want to take another person's body for her survival, hearing Replicant Yonah's constant cries for her father/brother from her body. After confirming that Nier is the father/brother in question, Yonah decides to respect their love and commits suicide by standing in sunlight. Despite Gestalt Nier's pleas, she sadly apologizes and tells him she loves him as she dies.
Her spirit reappears during Ending B to give her father/brother the cookie from the prologue.
- Yonah is the only character seen as a true human in the main game.
- She is the only character in NieR to appear only in the prologue and part two.
- Her role in the story mirrors a discarded idea Yoko had for Furiae in Drakengard.