Route A: Unlike Replicant, this was pretty standard and short. It is basically about the build up for 2B and 9S's relationship. It is where you start to see the pain 2B is having to see 9S be killed in front of her 2 times. Even with her killing him in the finale. This is crucial for later on.
Route B: Similar to Replicant in the next route you get to see things from a different perspective slightly. This time from the view of the machines. But it was nowhere near as gut punching as it was for the shades in Replicant. But beyond that, you were just repeating everything with just controlling 9S instead of 2B unless he was in the bunker. It was a nice change of pace in terms of gameplay but the hacking does become repetitive. So I could see where this route could feel meh to some people.
In these two routes you get cool references to Replicant. First you see the machines wearing masks like the people in Facade did in replicant. And in their arena you get to see them talk about those people that exist and all the rules they have. Even making jokes about some rules being unnecessary.
The big one is Emil. In his side quest you learn that when the machines came to earth he was forced to make copies of himself, but at the cost of his memories. The raw emotion lets you thinking what where are all those key places in Replicant now? Well, we get to learn one such place. To finish his quest you take the elevator down the shopping mall where it leads to Kaine's old home/place. Filled with lunar tears. After playing Replicant that shyt hits you hard.
The last bit was Popola and Devola. At first you are confused AF since you killed Devola in Replicant at the end and Popola's being uncertain. But towards the end of part two you learn that these two aren't the same ones. However, it is a model. But due to Replicant's Popola and Devola the other ones or at least these ones were forced to feel guilty of what the Replicant versions did. Even if you couldn't stand them in Replicant, you feel sad for them because they were forced to feel guilty for something that a different version of them did. Kinda fukked up.
Rest of game: So the rest of the game is where the big money is. The machines inflict a virus that spreads across all Androids on the network. And basically eventually when 2B and 9S split up, 2B is kinda left in a situation where she is fukked up. Because she can't back herself up, so she knows her time is up. Which leaves her asking A2 to kill her. Unfortunately 9S takes it the wrong way and just sees A2 killing 2B.
I'll be honest 2B does feel like easily the worst of the 6 main characters in Nier. But not bad just not on the same level as the other 5. (Kaine, Nier, Emil, 9S and A2) But the big thing that does happen is this part is that slowly A2 starts to open up and be more friendly. Which feels like mainly due to 2B's influence on her, which was a nice touch. Similar to Kaine, but still keeping her attitude that you see early on. The real crusher is when you learn that the backstory with Anemone. Basically they were sent on a suicide mission to test out what became the models that 2B was. Overall A2 is great. Just a notch lower than Kaine, who to me is the stand out character in the series so far.
Back to 9S this situation fukks him up. He already learns that 2B was forced to kill him time and time again after every mission. But never gets to tell 2B about this. Then once he sees A2 kill 2B from his perspective it destroys him.
Now the most interesting bit here is that 2B was routinely forced to kill 9S at the end of each mission. She supposedly falls for him and the same for 9S's feelings for 2B. But his memory gets reset, but not for 2B. So in fact this cycle continues again and again. To the point where we see how cold 2B seems at the beginning of the game. That isn't the real her, but the real her is the one right before she dies. She seems much more cheerful. It also seems clear that the memory wipes weren't totally affective on 9S. Since he easily falls for 2B at the beginning of the game. So it seems like a never ending cycle of 2B killing the one she loves over and over again. That whole situation is depressing af
Now 9S is conflicted here because he clearly loves 2B and wants revenge on A2. But he does have some anger since 2B has always killed him. You see this in the scene with all the 2B's in the tower. Where he says basically "Finally I get to kill you." I'll be honest I wished 9S didn't become as edgy as he became. I was hoping it would be something like Nier. Where he becomes a darker person, but it never affected his relationship with Kaine and Emil. Although maybe its because of those two friends that Nier didn't become as fukked up as 9S. Who was all alone.
Ultimately the endings were pretty straight forward. A2 sacrifices herself to destroy all the machines since all the people she grew fond of were long gone by now. Once you learn of A2's past this feels very satisfying as an ending. She does save 9s, but I assume at the cost of his memories. So in a more realistic sense it has the most realistic good way to end this.
Ending D is a lil weird. Where A2 and 9S kill each other. But this is what 9s ultimately wanted because he didn't want to lose his memories of 2B. Despite what secondary thoughts he might have had when he learned the truth. Now without Ending E this just feels depressing to me. Thank god it wasn't the final one ending to the game.
Ending E gets you the feel good ending where 2B, A2 and 9S get brought back to a world without machines. It is THE canon ending. And for a feeling good ending it hit all the checkmarks and felt rewarding enough. Could they make a sequel sure it did take 7 years for a sequel from Automata from the OG Nier to come out. Although I wouldn't press any bets.
While the story is fantastic there is a lot of digesting to it. I still prefer Replicant if I had to pick between the two.