There are four endings in NIER.
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Ending A
Ending B
Replicant Nier is about to kill Gestalt Nier. He gazes at the Shadowlord, now having lost all hope. Replicant Nier hesitates for a second before dealing a final blow. The scene then changes to Gestalt Nier scrunched up, weeping to himself - alone in a white void - as he regrets all the hardships he put Yonah through. A flashback occurs, with Yonah and himself alone in the grocery store. He tells her that he isn't hungry, while Yonah tries to force him to eat something. The scene reverts back and images of enemies, that Replicant Nier, killed gaze at him while he cries to himself. Gestalt Yonah, in her young form comes to greet him and thanks him for always being there with her, and shares the cookie with her father.
Emil, who survived the blast, crash lands in the desert. Now just a head, he goes out to search for Nier and Kainé, bouncing and rolling into the distance.
Ending C
The game's third ending has to do with the future of Kainé. After she relapses, Tyrann explains to Nier how he can save her. Either by killing her, or forgoing his entire existence for her. If the player chooses the first option, Nier kills Kainé and lives with Yonah until they both die from the Black Scrawl.
Ending D
If the player chooses to sacrifice his entire existence for Kainé, the player's data is erased and everyone forgets he ever existed. Nier disappears, while Yonah thanks Kainé for saving her. Kainé has a flashback of Nier and mentions that it feels like she found something special.
Ending E
In "Ending E", told in Grimoire Nier, after the Shadowlord disappeared, a program to reset the entire Replicant system begins its execution in the Forest of Myth, and Kainé goes to destroy it. The forgotten Nier is reunited with Kainé, as a young boy, reconstructed with the “memories” that the tree had of his first visit to the Forest of Myth.