The following contains spoilers for episode 3 of NieR Automata Ver1.1a, now streaming on Crunchyroll.
Last week, we left off with 2B and 9S coming to The Resistance's rescue, much to Lily's dismay. For a quick recap, previously one of the machine's discovered human knowledge and became enamored with it to the point where it began imitating human behavior, namely planting a garden and contemplating the meaning of life.
Meanwhile, The Resistance continues to struggle against their ongoing battle with the other machine lifeforms. After an abnormality is discovered on Earth, and communication is cut off, 2B and 9S are sent to the surface to investigate the cause. There they rendezvous with the others, but Lily seems to be more familiar with the YoRHa units than she lets on.
Regrouping
2B and 9S help the group get their bearings as they retreat to The Resistance camp. It's at that time, 2B takes note of Devola and Popola, maintenance model androids who are on the front lines, though one of the members is quick to brush it off, saying it's their choice. Observing the group's demeaning attitudes against the two androids during episode 2, it's safe to say there's some beef going on between them. Once they enter the camp, we get an insight into their everyday lives on Earth. On a nearby radio, 24D cheerfully reads the "Morning Letter", essentially acting as a DJ for the androids nearby; while merchants try to one-up each other on who has the better product that they can sell to outsiders. A side note, the "D" designation refers to "Defender", but in this case, 24"D" is the "D"J.
It's at this time that the duo are told by Lily that The Resistance had been requesting reinforcements from the Council of Humanity for a long time, and believe that 2B and 9S were sent there to help them. We also meet a new character, Jackass, an enthusiastic scientist who offers to help them in their investigation.
Bringing Out Your Inner Traveler
The trio heads to the location of the abnormalities 2B and 9S were assigned to, though Jackass figures out their true reason for coming to Earth wasn't for assistance. They are then ambushed by a group of machines wearing masks eerily similar to Sechs's in NieR: Replicant. 9S uses his hacking skills to destroy the leader from the inside, however, he's met with an image from the distant past, specifically Fyra's and Sechs's wedding. While this catches him off guard, he's able to successfully disable the source and the machines are defeated. But one flees in terror, which is unusual for a machine.
As the group continues forward, the Pods take note of their new surroundings: A Housing Complex from the past. It's quiet, but it's far from empty, as communication with the rest of YoRHa is cut off, and they discover countless android bodies and machines with hair - another abnormality. But it doesn't stop there either, as 2B and 9S are separated from Jackass and fall into an underground hideout where the rest of the machines reside.
Humanity Without Humans
The two make a disturbing discovery when they're met with a group of machines imitating human mating behavior. But what's more, is that other robots are shown displaying conventional shows of affection, like cuddling and rocking a cradle - different "stages" of the pre- and post-reproductive process, for lack of a better term. 9S takes advantage of their distraction and launches an attack, but again, the machines go on the defense and form into circle or egg-like shape; and outcomes another machine. This time, however it resembles another android. 2B and 9S manage to fight him off, but from his wound, a rib pops out and forms into an identical model, before he takes his clone's body and retreats. This leaves the YoRHa units at a loss, both of questions and answers.
Animals Are [N]ot Cars
In the after credits puppet show, 9S once again shares his knowledge with us, this time educating 2B as well. He proposes riding boars to have the experience of riding an animal, but unfortunately forgot that animals don't have brakes, and end up crashing into the rest of YoRHa, triggering another joke ending. At least they won't have to obey orders anymore.
What Just Happened?
A lot happened in this episode, and even veteran gamers had a lot to take in this time around. But it was interesting enough for speculation and exposition from the last episode. It makes you wonder, "What exactly is human behavior?". Fear, love, and desire are a few to name, but anger, hate, and violence are as well. The machine life forms began to change their behavior in accordance with what content they consumed; but into something much more benevolent. Could it be that anger and hate is a learned behavior, but compassion is natural? This leaves the viewer thinking.
This goes for the adaptation as a whole, but this episode especially did well in presenting the NPCs in a more natural setting. Obviously, when playing a video game, NPCs will have certain dialogue, but only if you speak to them, and it wouldn't make sense for the player character in an adaptation to just mimic the player straight up. Two merchants approach 2B and 9S and offer their services and products, but make small talk first. Fans' commentary from past content is also taken into consideration here.
Shortly after the NieR: Automata game was released, players had questions on what 9S carried in the bag he wears on his back, Yoko Taro jokingly said he was carrying tissues, in response. Here in episode 3, he implies it's a secret - a cool callback and shout out to the audience. The puppet show, however reveals that he had an acorn in his bag. But Yoko Taro said otherwise. Then again, what use would 9S have for any of those?
Later on, we will discover that the two androids the pair fought at the end will call themselves, Adam and Eve - a reference to the first two humans in the Bible. In the story, Adam, the first human sacrifices a rib to birth Eve, the second human. The original NieR: Automata game showed the android, Eve being "birthed" from Adam's rib cage, but the anime made it more explicit that he came directly from a single rib. It's safe to assume that one of the books the machines were taking in knowledge from, was in fact the Bible.
Fun fact: episode 3's language code translates to, "Report: This may act as gospel, for us", a reference to the Gospel, a section also in the Bible.