Yoko Taro is highly celebrated for the overcomplex plots that he brings to life in his games. Drakengard and Nier are two franchises with convoluted stories that leave a lot to interpretation and constantly blow minds by revealing completely unexpected plot twists throughout the games.
Nier was considered an underappreciated gem due to the amazingly innovative storytelling format that did not get as much attention as Nier Automata. Luckily, the success of Nier Automata made Nier Replicant return to life in the form of an expanded remaster.
Although Nier Replicant is indeed an amazing game with interesting plot twists, it does have many unusual characters, gameplay mechanics, and interconnected stories. Players of Yoko Taro's games know these characteristics and this level of complexity will always cause some unsolved plot points when all is taken to account. Here are a few.
Warning: This article contains spoilers for some of the game's endings.
10 The Soulless Bodies Refuse Souls
At some point, it is clearly explained that the Replicants are the artificial bodies that were left behind so the Gestalts, souls of the real humans, would eventually have a body to return to. That shouldn't be much of an issue, considering that Replicants keep being remade upon their deaths.
However, considering that Replicants must use their Gestalts in order to have personalities and memories, it seems odd that the Replicants would not accept being united their missing half or why this would cause any issue since Replicants are empty husks.
9 The Shadowlord's Goal
This is one of the things in the plot that many players miss. The original Nier is turned into the Shadowlord in order to control the Gestalts. Most likely making most of the human souls, including Yonah's, go into a stasis-like state. That would be done in order to prevent the souls from becoming shades, something that Yonah was already turning into.
The idea was to wait for the White Chlorination Syndrome to vanish on its own, and then have the Gestalts returned to their Replicant bodies. The issue with this plan is the Black Scrawl disease, which caused Replicants to slowly die if their Gestalts were in the process of turning into a shade. This meant Yonah was condemned already.
8 The Black Scrawl Disease
It is not clear why, but the human souls were vulnerable to some sort of corruption. This was called Relapsing, the transformation of a Gestalt into a Shade. If a Gestalt was put into stasis while in the process of relapsing, the Black Scrawl would eventually show up in the replicant and nothing could be done about it.
The odd part about it is how it would affect the replicant's body. Shades were corrupted Gestalts, so it might make sense that Replicants can no longer be made out of shades. However, it makes little sense that a partially corrupted gestalt would give flu-like symptoms to Replicants.
7 The Grimoire Doesn't Always Turn People Into Shades
Nier was given a Grimoire Noir since he was supposed to be one of the people who could control other people's Gestalts. However, it is never clearly stated if that is also the reason he can safely touch his grimoire. It is made very clear that the Grimoires turn people into Gestalts, but most were straight-up turning into shades right after.
Nier carried the Grimoire around, kicked the book, and kept refusing its offers of more power. It is not very clear why, though. And as soon as Yonah tried to help Nier by touching Noir, she started her transformation into a shade.
6 Yonah Touched The Book
Civilization was ended. The Legion was finishing humanity off and those who were meant to live by separating themselves from their bodies were also hunting humans. It was pretty clear that using the Grimoire was making humans turn into crazy, mindless souls who hunted their own kin. This is why Nier repeatedly told his sister not to touch the book.
Yonah touched the Grimoire Noir because she wanted to help, but the Grimoire has never helped anyone around her. It makes little sense that she would do that after being attacked by what people turned into after touching Noir.
5 Grimoire Noir Makes Human Nier More Powerful
This is odd on its own. After many people turning into Shades for trying to use their copy of the Grimoire, Nier was very afraid of using it. The Grimoire was constantly offering power to him but he kept ignoring it. It was only when Nier had no choice that he accepted Noir's offer.
However, it is unclear if Nier was the only one who could use this power. It is very strange that no other copies of the Grimoire were able to help their owners. If it has something to do with Nier being able to control Gestalts, it does not seem like he was the only candidate.
4 Shades Can Be Killed
So humans prevented death by temporarily separating their bodies from their souls. Their souls, called Gestalts, eventually went mad and turned into what are called Shades. However, many shades are defeated by Nier right at the beginning of the game. He was just wielding what seems to be a pipe as a weapon.
Eventually, shades become different and unique. Not only they can affect things physically, but they also start wearing armor, wielding weapons, and taking unusual shapes. But more importantly. they die from being physically beaten down, even though they are but souls.
3 New Replicants Were Not Made
Apparently, Project Replicant failed because the future bodies of the Gestalts developed personalities and cultures of their own. However, Replicants were very unaware of many things. They were even unaware of how new life was made. The truth is that the twin droids who looked over the Replicants were in charge of making a Replicant son or daughter when needed. They would also recycle Replicants who died.
It is strange that the project failed due to replicants becoming self-aware. Also, it is a bit hard to understand why the twin droids wouldn't make new, recently created bodies for humanity.
2 The Shadowlord's Fight Seems Pointless
It is hinted in Ending A and Ending B that the Shadowlord meets his sister in the afterlife. In one of the endings, they share a cookie. On the other, they can be seen holding hands. If souls could live this whole time without a body, it is quite unclear why there was any need for the Gestalts to return to physical bodies.
But if there was an afterlife for the shades, the whole fight that the Shadowlord goes through is pointless. He fights for over a thousand years to be reunited with his sister and fails. However, his failure is what reunites him with her according to ending A and B.
1 Kainé And Nier Make Replicants Go Extinct
In Ending E, Kainé goes searching for Nier. That happens because Nier gives his life in order to prevent Kainé from being completely possessed by a Shade. That is already weird. There is no clear explanation as to why the main character has to disappear from existence to prevent the Shade to take over the party member.
Things get even weirder when Kainé, who for some reason remembers Nier, decides to bring him back by making a new Nier Replicant. She also destroys the facility in the process, assuring that no new Replicant would ever be made. But even before that, Nier was exterminating Shades, making many Replicants die from the Black Scrawl. The world without humans is one of the things that ties Replicant to Automata.