Yoko Taro’s Nier games are noted to be rather obtuse when it comes to exactly how to find all of their secrets. Getting the “best” ending on the original Nier game required players to go through the game multiple times, and Automata had the same process. However, one Nier Automata secret is still out there.
In particular, this secret (known only as “that” to the game’s designers) still has yet to be discovered. However, the development team hasn’t talked about what it actually is because it could apparently be bad. Exactly what that means, however, remains to be seen.
Nier Automata has 26 different endings, some of which are the actual progression of the narrative but many of which are also either joke endings or non-standard endings resulting from doing something in the game, such as refusing objectives or attacking vital NPCs, or even things like dying in the tutorial level.
However, even if players have uncovered the variety of different secrets in the game, like all of the endings, a boss fight against a large number of different Emil clones, and more, whatever Nier Automata secret that its developers have put in the game will likely stay hidden for a good while, either until someone actually stumbles upon it or the devs reveal it themselves.
The revelation of the last Nier Automata secret came as part of an interview with a number of different developers on the game, who each had something that they wanted to share about the game, such as how fans of the original Nier made Automata such a success, how they’d hoped to reach a million units but never expected two million, and other things like that.
So, if you own Nier Automata and have uncovered what you think are all of its secrets, keep looking! There’s no telling what the last Nier Automata secret will turn out to be.