In Episode 3 of NieR Automata, the anime delves even deeper into the complex world and characters of the game. The episode introduces two new characters, Lily and Jackass, who add more depth to the story and provide a new perspective on the ongoing war. Lily, a member of the resistance, is a strong and determined character who gives viewers insight into the struggles and motivations of her faction. Jackass, on the other hand, is a scientist with a passion for researching androids and machines, and her actions will have a major impact on the story.

The episode is primarily set in the desert, a familiar environment from the game. The machines in the desert repeat the same lines as in the game, revealing their sentience and questioning the nature of their existence. The episode also features a mysterious, camouflaged and masked machine that stalks 9S and 2B, leading them to a shocking discovery. They encounter a group of machines imitating human traits such as sex and parenthood, and ultimately, their fusion gives rise to a mysterious figure. This entity turns out to be Adam and Eve, the main antagonists of the series.

The episode also showcases a memory hack by 9S from the first NieR game, NieR Replicant. This memory of a sand city within the heart of a machine raises questions about the origin of their sentience and their connection to the human world. The episode ends on a cliffhanger, leaving the viewer eager to see how the story will unfold and what impact the new characters and their actions will have on the narrative. The episode prompts thoughtful questions about the nature of existence, the consequences of war, and the relationship between humans and machines.