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So on all the usual sites I go to for trophy hunting, NieR: Automata is listed as having no missable trophies because once you complete the third playthrough, you are able to buy the trophies from an npc. However, I would like to get all the trophies the legitimate way and earn them. So are there any missable trophies if I do not purchase them?

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Yes. There is just one missable trophy if you are morally opposed to using the trophy shop.

The trophy is Transcendent Being and it is awarded for attaining all 26 endings. The only missable ending is ending Y. This is due to the fact that ending Y is tied to failing a side-quest. The side quest is

Emil's Determination

To get the ending, you need to lose the boss fight in the desert at a specific point.

Near the end of the fight, one of the giant Emil heads starts a countdown timer before it explodes (and subsequently destroys the Earth), you need to simply let the timer run out. This will lead to ending Y. If you kill the Emil head (which finishes the side quest) before getting this ending, ending Y is not possible to get.

Since side quests can not be repeated on a save file, if you complete this quest without getting ending Y, you will either have to redo everything and try again or cave in and use the trophy shop.

However, I wouldn't recommend redoing everything to get this ending since to get it, you need to collect and max out every weapon in the entire game, which takes a very long time.

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There are two missable trophies if you insist on not using the trophy shop.

The first is Transcendent Being, which you can miss if you miss ending Y.

The second is Supreme Support Weapons, which you receive for upgrading all your pods to max.

One of the required materials, Powerup Part S, is missable. You need to acquire 3 of these, 2 of which can be obtained from quests. The third can only drop from Gold Goliath Bipeds. These enemies spawn as part of a mini-event that doesn't appear under the quest tab, in which you must kill golden stubby robots guarded by either a Goliath or Tank in four locations, in order. You'll first encounter them in the City Ruins near the bridge leading to the Abandoned Factory, once they are killed they will spawn on the bridge in Flooded City, then they will spawn on the dunes just outside Desert: Housing Complex, and finally they will spawn on the bridge in the Flooded City again. They will continue to spawn at these first few locations until you defeat the final one in Flooded City, at which point you will no longer be able to encounter them again, so make sure you acquire at least one Powerup Part S from these Golden Goliath Bipeds before you kill the fourth golden stubby robot.

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    Thread necromancy, but it's the gold stubby bot that drops the Power Up S. If you do what I did my first playthrough and lure him away from the goliaths to spend 15 minutes beating on him, he'll "die" but won't explode and drop the powerup. He did respawn on the next playthrough though (probably because I couldn't beat the golden tank in the first run).
    – DerfK
    Oct 25, 2020 at 2:35

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