The Secrets of NieR:Automata: Hidden Endings, Bosses, Weapons, Rooms, and Missables

This article contains spoilers for essentially all of NieR:Automata, including Ending E, Emil’s late-game quest line, and the 3C3C1D119440927 DLC.

There is a wonderful problem with trying to write a guide to every secret in NieR:Automata: the game itself does not agree with the normal distinction between “the game” and “the secret stuff.”

Removing your operating system is an ending. Eating a fish is an ending. A traveling shopkeeper is also a level-99 superboss. His house is hidden at the bottom of a sewer, and robbing it twice is part of the route to another superboss. A statue that looks like scenery is actually a level-80 enemy. The game will sell you its trophies. There is a real developer cheat code hidden in the prologue that jumps almost straight to the postgame. A DLC arena contains a boss fight against the then-heads of Square Enix and PlatinumGames.

And for years after release, the community was still willing to believe that somebody might have found another hidden church.

So this is not a chest-by-chest walkthrough. It is an attempt to collect the meaningful secrets: hidden endings, bosses, places, weapons, Pods and programs, unusual unlock systems, DLC secrets, mechanical jokes, and Easter eggs that either give you something unique or are easy to walk past without realizing they exist.

The good news is that Automata is much kinder to completionists than it initially appears.

First: what can you actually miss forever?

Very little.

After you complete Route C and obtain Ending C or D, NieR:Automata unlocks Chapter Select. Unfinished sidequests that disappeared because the story advanced can then be revisited in the chapter where they were available. The NieR Wiki’s quest documentation states this explicitly: quests appear and disappear according to the current chapter, but unfinished quests can be revisited through Chapter Select after completing the game. (NieR Wiki — Quests)

That changes the meaning of “missable” considerably.

I use five labels in this guide:

Permanent: you can lock this out on the current save file even after Chapter Select.
Destructive choice: optional, but doing it really does destroy something you may care about.
Route-window: it can disappear during normal story progression, but Chapter Select lets you return later.
Postgame-safe: hidden, but you can comfortably clean it up after unlocking Chapter Select.
DLC: requires the 3C3C1D119440927 content; this DLC is bundled with the Game of the YoRHa / Become as Gods / End of YoRHa releases, although availability details vary by platform. Square Enix describes it as three colosseums plus costumes and additional sidequests. (Square Enix)

There is one warning I would put above every other completionist note in this article:

Ending Y is the one famous permanently missable ending. During Emil’s Determination, see Ending Y before you finish the quest.

Once Emil’s Determination is completed, it cannot be replayed through Chapter Select. If you stop the final self-destruction before ever seeing Ending Y, that ending is gone on that save. (NieR Wiki — Emil’s Determination; NieR Wiki — Ending Y)

There is one other irreversible-looking choice worth understanding, but it is voluntary: the save-data sacrifice after Ending E. You do not have to delete your saves to obtain Ending E. If you accept the later offer to sacrifice your data, however, the game really does erase the save slots. (GameFAQs — Ending E save data)

Those are the two points at which I would slow down and read the screen twice.

The 26 base-game endings are themselves a secret system

The base game has endings A through Z. A through E form the main story; F through Z are alternate, failure, joke, or hidden endings. The 3C3C1D119440927 DLC adds one more ending marked ◬, bringing the total to 27 when the DLC ending is counted. (RPG Site — Endings; NieR Wiki — Endings)

Endings A through E

Ending	How to unlock it	Missability
A — flowers for m[A]chines	Finish the first main route.	Story-required.
B — or not to [B]e	Continue the same save after A and finish the second route.	Story-required.
C — meaningless [C]ode	In the final confrontation of Route C, choose A2.	Postgame-safe; use Chapter Select for the other choice.
D — chil[D]hood’s end	In that same confrontation, choose 9S.	Postgame-safe.
E — the [E]nd of YoRHa	Have C and D on the same save, then continue into the altered credits sequence and accept the Pods’ request to keep fighting for the characters’ survival.	Postgame-safe. Deleting your saves afterward is optional.

(RPG Site — Endings)

The Ending E distinction is important because it is often summarized badly. The ending and the sacrifice are not the same unlock condition. You can finish Ending E, decline to give up your data, and keep using Chapter Select. If you later decide you want to make the sacrifice, you can replay the Ending E sequence. (GameFAQs — Ending E save data; GameFAQs walkthrough — Ending E)

Missability: Ending E itself is not permanently missable. The save sacrifice is a destructive choice.

Endings F through Z

These are where Automata starts treating disobedience as a collectible.

Ending	Trigger	Permanently missable?
F — mission [F]ailed	During 9S’s first OS-repair sequence, let the recovery timer expire.	No.
G — hun[G]ry for knowledge	The first time you control 9S, leave the mission area instead of carrying out the objective.	No.
H — a mountain too [H]igh	When the second major Goliath battle calls you back, run away from the battlefield.	No.
I — no [I] in team	After the Copied City boss, leave 9S instead of going to him.	No.
J — bad [J]udgment	At the first meeting with the religious machines in the Abandoned Factory, attack them.	No.
K — aji wo [K]utta	Accept Jackass’s mackerel and eat it.	No.
L — [L]one wolf	Abandon the final battle area near the end of Route A or B.	No.
M — break ti[M]e	In Route C, fail to go help Pascal’s Village when asked.	No.
N — [N]o man’s village	Kill the non-hostile machines throughout Pascal’s Village.	No.
O — just y[O]u and me	At the beginning of Route C, abandon the battlefield.	No.
P — corru[P]tion	During Route C, allow 2B’s logic-virus infection to reach 100%.	No.
Q — [Q]uestionable actions	As 9S in Route C, abandon the objective to find 2B.	No.
R — mave[R]ick	As A2, attack Pascal’s refugees in the Abandoned Factory.	No.
S — city e[S]cape	During the Tower assault, abandon Devola and Popola.	No.
T — fa[T]al error	Unequip the OS Chip.	No.
U — deb[U]nked	Self-destruct while inside the Bunker.	No.
V — reckless bra[V]ery	During the Tower assault, refuse to hack the Tower and allow the defenders’ situation to collapse.	No.
W — broken [W]ings	Die during the Route A prologue.	No.
X — time to rela[X]	When control switches to A2 during 2B’s crisis, run away instead of helping.	No.
Y — head[Y] battle	During the final fight of Emil’s Determination, allow the Emil clones to complete their self-destruction.	YES. Get this before completing the quest.
Z — over[Z]ealous	When A2 first encounters Pascal, kill Pascal.	No.

The trigger list above is cross-checked against RPG Site’s A–Z guide; the special status of Y is independently documented by the NieR Wiki. (RPG Site — Endings; NieR Wiki — Ending Y)

The practical completionist method is therefore very simple: after Chapter Select unlocks, collect F–X and Z whenever convenient. Save Y for the Emil section below and follow the order there.

DLC ending ◬

The DLC contains a 27th ending, written as a triangle-like ◬ rather than another letter.

Complete the three colosseum quest lines from Mysterious Letter. You will then receive Mysterious Invitation, which points below the Amusement Park. There, watching the memories of Plato 1728 leads into the amazarashi music video Deserving of Life and awards Ending ◬. (NieR Wiki — Mysterious Letter; NieR Wiki — Mysterious Invitation; NieR Wiki — Ending ◬)

Missability: DLC, postgame-safe.

The Emil rabbit hole is the game’s largest chain of secrets

If Automata had one conventional “ultimate secret quest,” this would be it. It begins with flowers and ends with a level-99 apocalyptic boss battle whose failure condition is the only permanently missable ending in the base game.

Step 1: Emil’s Memories and the five Lunar Tears

After completing the Forest Zone main story, find Emil’s traveling shop in the City Ruins and interact with him. Return to the Shopping Center and inspect the Lunar Tear there to begin Emil’s Memories. The quest then sends you to the remaining Lunar Tears in the:

Shopping Center
Forest Zone
Amusement Park
Desert Zone
Flooded City

(NieR Wiki — Emil’s Memories; Gameranx — Lunar Tear guide)

After all five are found, Emil gives you an Elevator Key. Use the strange elevator at the Shopping Center.

At the bottom is one of the game’s best secrets: a reconstruction of Kainé’s shack, surrounded by Lunar Tears. The location is explicitly listed as the destination of the Shopping Center’s keyed elevator, and the Lunar Tear documentation identifies the hidden shack and garden. (NieR Wiki — Shopping Center; NieR Wiki — Lunar Tear)

This is more than an Easter egg. It unlocks the Lunar Tear accessory/trophy and gives the game one of its most overt physical links to the original NieR.

Missability: route-window. The quest has a normal-story deadline before the Grün sequence, but Chapter Select lets you return to its valid chapter later. (NieR Wiki — Emil’s Memories)

Step 2: find Emil’s actual house and rob it

In the City Ruins crater, find the large sewer pipe with water flowing from it. Inside is an elevator leading deep underground. Follow the long cavern route to Emil’s residence.

Take an Emil Mask from the display in his house. Return to the surface and talk to traveling Emil again. He will complain about a thief and mention increasing his security.

Now return to the house as 9S. A hackable chest will be waiting. Open it and leave.

Emil catches you.

The result is the first level-99 Emil superboss. Defeating him awards the Emil Heads combat bracers and the Naughty Children trophy/achievement. The requirement for 9S comes from the hack-locked second theft. (Gameranx — Emil superboss; GameFAQs — Emil fight)

Missability: postgame-safe. It requires 9S, so it cannot be completed during the first 2B route anyway.

Step 3: find Masamune and upgrade every weapon to Level 4

The next Emil quest stays hidden until you have upgraded the full weapon collection to Level 4. Ordinary weapon shops stop at Level 3, so this quietly requires another secret.

Go to Forest Castle: Royal Chamber. Head right onto the broken bridge, drop to the lower walkway, move left, and pull the large block from the wall. Behind it is Masamune, the hidden blacksmith who can perform Level 4 weapon upgrades. (NieR Wiki — Forest Castle; 30 Something Gaming — Masamune)

Upgrade any weapon to Level 4 and Masamune also gives you Cruel Lament. (RPG Site — Weapons)

The all-weapons requirement includes the Emil Heads from the previous secret boss; the NieR Wiki specifically notes that Emil’s Determination remains hidden until every weapon is at Level 4, including Emil Heads. (NieR Wiki — Emil’s Determination)

Missability: postgame-safe. Masamune’s room remains accessible.

Step 4: Emil’s Determination and the second secret boss

Once the weapon condition is satisfied, Emil appears at the Shopping Center with Emil’s Determination. Follow him to the Desert Zone and fight the enormous replicated Emil forms. (NieR Wiki — Emil’s Determination)

This is the point where a completionist can make the game’s one truly nasty mistake.

Near the end of the battle, the last Emil begins a self-destruct sequence.

For Ending Y, do nothing. Let the countdown finish. The explosion produces head[Y] battle. (NieR Wiki — Ending Y)

Then reload the save from before the fight, repeat the battle, and this time stop the self-destruction so that Emil’s Determination actually completes.

Do those in the opposite order and the completed sidequest cannot be replayed; Ending Y is then inaccessible on that save. The NieR Wiki calls this out directly. (NieR Wiki — Emil’s Determination)

Missability: Ending Y is permanent. Save before this fight.

The hidden weapons that are actually hidden

Automata has a large weapon collection, but most weapons are purchases, obvious quest rewards, or story equipment. Calling every one of them a “secret” would make the word useless.

The following are the weapons whose acquisition is genuinely concealed behind a strange location, Scanner search, hacking gate, unusual shop state, or secret chain. RPG Site’s full weapon guide is the main cross-check for this section. (RPG Site — Weapons)

Small swords

Iron Pipe — Fish in the sewers. Yes, the fishing minigame can pull a weapon out of sewage.

Phoenix Dagger — Search under the bridge connecting the Shopping Center area and Forest Zone.

Engine Blade — Find the hidden chest in the Abandoned Factory underground near the end of Route A. This is Noctis’s weapon from Final Fantasy XV; at Level 4 its Shift Avoid ability even changes the visual style of your evade and damage numbers. (RPG Site — Weapons)

Cypress Stick — Near the Forest Castle entrance, use the courtyard pillars as a platforming route to the hidden chest. Its Level 4 Hero Sigil changes damage-number and chest presentation in a deliberate Dragon Quest joke. (RPG Site — Weapons)

Faith — Located inside the Soul Box resource unit in the Flooded City during the late game.

Large swords

Iron Will — Use the Scanner in the Flooded City rather than looking for a normal chest.

Phoenix Sword — On the roof of the City Ruins building where the androids first arrive on Earth; the chest requires 9S’s hacking.

Cruel Blood Oath — Hidden in a hack-locked underground section of the Desert Zone.

Spears

Phoenix Lance — Another Scanner find, this time around the center of the Desert Zone.

Beastcurse — In a hackable chest high in the Forest Castle.

Dragoon Lance — Hidden in a cave below the Forest Zone ravine.

Type-3 Lance — On top of an isolated broken building in the Flooded City.

Virtuous Dignity — Enter the sewer route near the Amusement Park and find the additional ladder leading to a secret area rather than simply following the normal exit.

Cruel Arrogance — In the Abandoned Factory cult area, above the conveyor route, behind a gate that requires hacking.

Combat bracers

Demon’s Cry — Ride the elevator below the Amusement Park castle and hack the chest near the wall of televisions.

Type-40 Fists — A hackable chest is hidden almost comically close to home: beside the Resistance Camp access point.

Virtuous Grief — Hidden at a small shrine in the Forest Zone, southwest of the access point near the upper river.

Cruel Lament — Upgrade any weapon to Level 4 with Masamune; he gives it to you.

Emil Heads — Complete the first level-99 Emil fight after robbing his house twice.

Type-3 Fists and Angel’s Folly — Emil’s shop inventory depends on the route his vehicle is running. RPG Site records both as purchases available when Emil is operating near the Resistance Camp rather than his ordinary route. (RPG Site — Weapons)

Missability for this entire section: postgame-safe. Some are inaccessible until 9S or a late-game chapter, but Chapter Select makes them recoverable. The one reason the list matters before Emil’s Determination is that you ultimately need the whole weapon collection at Level 4 to expose that quest.

There are two additional Pods hiding in the world

You start with Pod A, the Gatling model. The game never forces the other two into your hands.

Pod C — Missile: search the Desert Zone near the Oil Field / outer edge of the central desert area. It appears as a world pickup.

Pod B — Laser: go to the Flooded City coast and fish. Eventually your catch will be a Pod rather than a fish.

Multiple completion guides agree on the strange split: C is the desert pickup, B is the Flooded City fishing reward. (GameFAQs walkthrough — Pods; Cheat Code Central — Pods)

Once you have all three, each can carry a different Pod Program, and holding the program button can charge certain programs across multiple Pods.

Missability: postgame-safe.

All 17 Pod Programs, and where the non-obvious ones come from

There are 17 Pod Programs. One is your starting program, one arrives through the story, six are ordinary purchases, six are sidequest rewards, and three are easy-to-miss Route C world pickups. GameFAQs has a concise all-17 breakdown that matches this structure. (GameFAQs — all Pod Programs)

Pod Program	How to obtain it	Missability
R010 Laser	Starting program.	None.
A170 Scanner	Story progression.	None.
R020 Mirage	Buy from the Bunker terminal / Resistance Camp maintenance shop.	Postgame-safe.
R030 Hammer	Same shop.	Postgame-safe.
R040 Blade	Same shop.	Postgame-safe.
R050 Spear	Same shop.	Postgame-safe.
R060 P Shield	Same shop.	Postgame-safe.
R070 M Shield	Same shop.	Postgame-safe.
A140 Gravity	Reward for Retrieve the Confidential Intel.	Route-window; Chapter Select recovers it.
A080 Wave	Reward for The Wandering Couple.	Route-window.
A090 Wire	Reward for Amnesia.	Route-window; 9S-related quest.
A110 Slow	Reward for Data Analysis Freak 2.	Route-window.
A120 Repair	Reward for Sorting Trouble 3.	Route-window.
A130 Bomb	Reward for Find a Present.	Route-window.
A100 Decoy	Route C: beside a YoRHa corpse on the high bridge between City Ruins buildings near the original landing route.	Route-window.
A150 Volt	Route C: beside a YoRHa corpse in the Amusement Park tank courtyard.	Route-window.
A160 Missile	Route C: beside a YoRHa corpse on the containers near the final outdoor stairs of the Abandoned Factory.	Route-window.

(GameFAQs — all Pod Programs)

The last three are the dangerous ones for a blind player because nothing announces that new programs have appeared in old locations. Fortunately, they are exactly the kind of thing Chapter Select is good at cleaning up.

Masamune’s room contains a second secret: weapon stories have Level 4 endings

Finding Masamune is mechanically important because he is the Level 4 blacksmith, but the weapon upgrades carry a narrative reward as well.

Each weapon has a short story attached to its upgrade levels. If you stop at Level 3, you stop before the last entry. The secret blacksmith is therefore also the gate to the final page of every weapon story.

That matters disproportionately in a Yoko Taro game. Some of the most direct connections to earlier NieR material sit in item and weapon text rather than main cutscenes.

Missability: postgame-safe.

The Amusement Park’s golden rabbit is not a statue

The enormous golden rabbit in the Amusement Park entrance can sit there for dozens of hours looking like scenery.

It is a level-80 enemy.

Deal enough damage to the statue and it eventually wakes up. As 9S, hacking it is vastly more practical than trying to chew through its health normally, especially while underleveled. The hidden enemy became a famous late-game experience farm because each successful hack and eventual kill gives a large amount of experience. (GameFAQs walkthrough — Golden Bunny; Arqade — Golden Bunny)

This is a particularly good Automata secret because the object was in front of you the whole time. Nothing new spawns. The scenery simply turns out to have had a health bar you could not see yet.

Missability: postgame-safe.

The secret trophy / achievement shop lets you buy achievements with G

After completing the late-game route that unlocks Chapter Select, return to the Resistance Camp and talk to the Strange Resistance Woman, the NPC with the round machine-like head.

One of her dialogue options is “Request unlocking you-know-what.” It opens the Secret Shop, where a large portion of the game’s trophies/achievements can simply be bought with in-game currency. GameFAQs documents 28 numbered trophies in the shop; PlayStationTrophies notes that non-story trophies outside the A–E ending set are purchasable, generally for 50,000G to 200,000G each. (GameFAQs — Trophy Shop; PlayStationTrophies — Trophy Shop)

This is not a joke menu that pretends to award them. It awards the platform trophy/achievement.

It also means that the trophy for collecting all A–Z endings can be purchased even if you do not want to do the enormous weapon-upgrade chain required to reach Ending Y. Buying the trophy does not add Ending Y to your save file, however; it merely unlocks the achievement. (GameFAQs — Transcendent Being)

Missability: postgame-safe. On Nintendo Switch, the platform has no system trophy equivalent, so the achievement system is absent there. (NieR Wiki — Achievements)

Two deliberately ridiculous hidden achievements

If you want to earn them rather than buy them:

What Are You Doing? — Make the camera trigger 2B’s push-away reaction while trying to look under her skirt 10 times. The achievement description coyly calls this “2B’s secret discovered 10 times.” (NieR Wiki — What Are You Doing?)

Not That I Mind… — Play for one hour as 9S without his shorts. The Dress Module can make this easier. (NieR Wiki — Not That I Mind)

Neither is permanently missable, and both can be bought from the Secret Shop on platforms that support achievements.

The prologue contains a real cheat code that skips almost the entire game

This may be the most literal secret in NieR:Automata.

In January 2021, modder Lance McDonald publicized what was widely described as the game’s “final secret”: a developer code that had survived undiscovered for years. WIRED later noted that the game’s official Twitter account confirmed the feature-unlock code as one of Yoko Taro’s hidden gems. (WIRED — the final secret)

The code can be entered immediately after the first major boss encounter in the factory prologue, at the moment 9S says he will scout ahead.

Go to the back of the boss arena and stand between the two sets of three barrels. Hold R2 and enter:

Up, Down, Up, Right, Left, Square, Circle, Triangle, Cross

On the original PlayStation control notation:

R2 (held) + ↑ ↓ ↑ → ← □ ○ △ ✕

GameFAQs documents the location and sequence and reports that successful entry fades to black, jumps to a post-credits state, and unlocks Chapter Select, Debug Mode, and the Debug Room. (GameFAQs — secret code)

This is not the sort of cheat I would recommend on a first playthrough. It is interesting precisely because it lets the software behave as if you had progressed far beyond what your save has actually experienced. Use it as a curiosity, a challenge-run tool, or a way to poke at the game after you already know what it is skipping.

Missability: none. It is a cheat, not a collectible.

Debug Mode and the Debug Room

The secret code above can unlock the debugging features absurdly early, but they also become available through late-game completion without using the code.

The important distinction is that Debug Mode is not normal progression. It gives you developer-like control over game state and combat setup rather than another canonical sidequest. If your goal is to discover story content in the intended order, leave it until the end.

Missability: none.

The DLC hides three arenas, a Plato story, and two company presidents

Square Enix’s own support documentation for 3C3C1D119440927 lists the three character outfits and explicitly notes two additional battles against then-Square Enix CEO/president Yosuke Matsuda and PlatinumGames president Kenichi Sato. (Square Enix Support)

The DLC begins with Mysterious Letter, which gives coordinates leading to three previously inaccessible elevators:

Trial of Sand — Desert Zone
Gambler’s Colosseum — Flooded City
Underground Colosseum — Forest Zone; this arena is 9S-specific

Completing the three arena quest lines unlocks Mysterious Invitation, the secret basement below the Amusement Park, the memories of Plato 1728, the amazarashi video, and Ending ◬. (NieR Wiki — DLC; NieR Wiki — Mysterious Invitation)

The CEO boss fight

Inside the Gambler’s Colosseum, repeatedly bother the Resistance staff member about fighting “you-know-who.” Persistence eventually unlocks the joke superboss battle against Matsuda and Sato. The DLC documentation records the fight and rewards including the CEO-themed masks/bullets. (NieR Wiki — DLC; NieR Wiki — Gambler’s Colosseum)

It is one of those developer jokes that sounds invented when summarized: keep pestering an NPC in the secret gambling arena until Square Enix and PlatinumGames management come down to beat you up.

It is real.

Missability: DLC, postgame-safe.

Some sidequests are effectively secret lore rooms

There are 60 base-game quests, and calling all 60 “secrets” would just duplicate a quest guide. The NieR Wiki notes that most are optional, while a subset reward weapons and Pod Programs. (NieR Wiki — Quests)

A handful deserve special mention because what they open is stranger than the quest marker suggests.

Treasure Hunt at the Castle opens the Forest King’s graveyard

The Forest Castle contains a locked graveyard area tied to Treasure Hunt at the Castle. Completing the castle’s treasure-hunt sequence eventually gets you behind the door and to the long-dead Ernst, watched over by the Gravekeeper. The Forest Castle location guide lists the graveyard as a quest-locked point of interest. (NieR Wiki — Forest Castle)

Missability: route-window.

Heritage of the Past is one of the game’s strongest links to the first NieR

This Desert Zone archaeology quest rewards the Spear of the Usurper and, more importantly, gives contextual clues about what the desert ruins actually are. The weapon reward is independently listed in the full weapon guide. (RPG Site — Weapons)

The quest is easy to leave half-finished because its artifacts are found with the Scanner over a broad search area.

Missability: route-window.

Gathering Keepsakes revisits the Lunar Tear location

Once Kainé’s shack has been opened through Emil’s Memories, later story/quest content can reuse the location. This is one reason to treat the Lunar Tear chain as more than a trophy detour: it adds a real place to the world that other scenes can inhabit. The Shopping Center location documentation notes that 9S returns to the elevator as part of Gathering Keepsakes. (NieR Wiki — Shopping Center)

Missability: route-window.

The hacking arcade is an unlock many players forget exists

After finishing the initial route and beginning Route B, access points gain an Arcade option that lets you replay hacking minigames you have previously encountered. GameFAQs lists the Arcade as an unlock after the first playthrough when Route B begins. (GameFAQs — secret code / unlockables)

It is easy to miss because hacking starts as a combat mechanic, not something the game initially presents as a collectible set of arcade stages.

Missability: none.

A handful of crossover and series references are hidden in the equipment and scenery

Not every Easter egg has an unlock condition, but several are substantial enough that a secrets guide feels incomplete without them.

Kainé’s shack and Lunar Tears

The place unlocked by Emil’s Memories is modeled after Kainé’s home from the original NieR, and its Lunar Tear garden is a direct continuation of one of that game’s defining images. The in-game location documentation identifies it as Kainé’s Shack. (NieR Wiki — Lunar Tear)

Engine Blade

The Engine Blade is the royal weapon associated with Noctis in Final Fantasy XV. Automata hides it in the Abandoned Factory. Its special Level 4 presentation changes the dodge effect and damage-number style rather than merely changing statistics. (RPG Site — Weapons)

Cypress Stick

The Cypress Stick is a Dragon Quest reference hidden behind Forest Castle platforming. Its Hero Sigil changes interface presentation in addition to combat behavior. (RPG Site — Weapons)

The weapon-story system itself

Many NieR and Drakengard references are buried in weapon descriptions that only become complete after Level 4. This is why the Masamune secret and the weapon collection are part of the story archaeology, not just a damage-maximization system.

One famous “secret” that is not in the game: the Copied City church

A secrets article about Automata written after 2022 should say this explicitly, because the story is almost too perfectly suited to becoming misinformation.

In 2022, a Reddit account named sadfutago posted footage of an elaborate hidden church apparently accessible from the Copied City. Nobody else could reproduce it. Dataminers could not find the assets. The existing modding tools were not believed capable of building something that elaborate.

For several days, the plausible explanations included an undiscovered retail-game secret, a strange version difference, cut content, an ARG, or a mod that represented a major technical breakthrough.

It was the last one.

The creators ultimately revealed that the church was a custom mod made by DevolasRevenge, Woeful_Wolf, and RaiderB. PC Gamer reported the reveal and later interviewed the creators about how the prank escaped its original small audience. (PC Gamer — church solved; PC Gamer — creators)

So there is no retail-game procedure for unlocking the Copied City church. If a guide tells you to perform some bizarre sequence to open it in an unmodified copy of Automata, that guide is extending the hoax.

The funny part is that the community had a rational reason to hesitate before calling it fake: a real, bizarre, postgame-skipping developer code had in fact remained undiscovered until 2021. WIRED made exactly that comparison while covering the church mystery. (WIRED — church mystery)

A practical “I want to see everything weird” route

If I were replaying Automata specifically to collect its secrets without turning the first 30 hours into checklist maintenance, I would do this:

Play Routes A and B naturally. Do sidequests that look interesting; do not panic if some disappear.
During the Forest-era portion of A or B, complete Emil’s Memories if you notice it. Visit Kainé’s shack.
Pick up Pod C in the desert and fish for Pod B in the Flooded City whenever convenient.
In Route B, use 9S to open hack-locked weapon chests that you remember passing as 2B.
Finish Route C and obtain either C or D, which unlocks Chapter Select.
Use Chapter Select to get the other of C/D, then complete Ending E. Decline the save sacrifice for now if you want to keep this completion file.
Sweep endings F through X and Z with Chapter Select.
Collect the hidden weapons and all 17 Pod Programs.
Find Masamune and bring the weapon collection to Level 4.
Complete the first secret Emil fight and obtain Emil Heads; upgrade those too.
SAVE. Start Emil’s Determination. Let the final clone self-destruct to get Ending Y.
Reload. Repeat the fight and prevent the self-destruction to actually finish Emil’s Determination.
Wake and fight the Golden Bunny if you have never done it.
Visit the Secret Trophy Shop, even if only to appreciate that it exists.
If you have 3C3C1D119440927, clear the three colosseums, see Plato 1728, obtain Ending ◬, and pester the Gambler’s Colosseum staff until the CEO fight appears.
Try the prologue developer code on a separate save or after you are done taking the intended progression seriously.
If you want the full Ending E ritual, replay it last and decide whether you actually want to sacrifice the save.

That route is deliberately relaxed because Automata gives you Chapter Select. The game wants to create panic about irreversible events; its completion systems are mostly designed to let you come back later.

The exception is Emil.

Save before Emil.

Compact missability checklist

Secret	Unlock	Missability
Endings A–E	Main routes + final C/D choice + Ending E credits sequence	Recoverable; Ending E save sacrifice is optional/destructive
Endings F–X, Z	Specific failures, departures, attacks, or equipment choices	Chapter Select recovery
Ending Y	Let final Emil clone self-destruct in Emil’s Determination	PERMANENTLY MISSABLE on that save if quest is completed first
Ending ◬	Complete DLC arenas + Mysterious Invitation	DLC; recoverable
Kainé’s shack	Complete Emil’s Memories and use Elevator Key	Route-window; recoverable
Emil’s house	Emil chain; sewer/elevator below City Ruins	Recoverable
Emil superboss #1	Steal mask, talk to Emil, return as 9S and hack chest	Recoverable
Emil superboss #2	All weapons Level 4; Emil’s Determination	Recoverable, but see Ending Y warning
Masamune	Hidden room under broken bridge in Forest Castle	Recoverable
Cruel Lament	Upgrade any weapon to Level 4 with Masamune	Recoverable
Hidden weapon set	Scanner finds, hacking chests, caves, platforming, Emil chain	Recoverable
Pod B	Fish in Flooded City	Recoverable
Pod C	Desert pickup	Recoverable
17 Pod Programs	Story + shop + six quests + three Route C corpse pickups	Recoverable
Golden Bunny	Damage Amusement Park statue until it activates	Recoverable
Trophy/Achievement Shop	Strange Resistance Woman after late-game completion	Recoverable; absent as platform trophy system on Switch
Prologue developer code	Barrel position + hidden button sequence	Always available; not a collectible
DLC CEO fight	Repeatedly ask Gambler’s Colosseum staff about “you-know-who”	DLC; recoverable
Copied City church	You don’t	Mod/hoax, not a retail-game secret

Sources

The links below are the sources actually used for the claims in this article. I favored sources that give concrete unlock conditions and cross-checked the most failure-prone claims — especially Ending Y, Ending E’s save deletion, the Emil chain, and the developer code — rather than relying on one giant fan list.

The Secrets of NieR:Automata: Hidden Endings, Bosses, Weapons, Rooms, and Missables

First: what can you actually miss forever?

The 26 base-game endings are themselves a secret system

Endings A through E

Endings F through Z

DLC ending ◬

The Emil rabbit hole is the game’s largest chain of secrets

Step 1: Emil’s Memories and the five Lunar Tears

Step 2: find Emil’s actual house and rob it

Step 3: find Masamune and upgrade every weapon to Level 4

Step 4: Emil’s Determination and the second secret boss

The hidden weapons that are actually hidden

Small swords

Large swords

Spears

Combat bracers

There are two additional Pods hiding in the world

All 17 Pod Programs, and where the non-obvious ones come from

Masamune’s room contains a second secret: weapon stories have Level 4 endings

The Amusement Park’s golden rabbit is not a statue

The secret trophy / achievement shop lets you buy achievements with G

Two deliberately ridiculous hidden achievements

The prologue contains a real cheat code that skips almost the entire game

Debug Mode and the Debug Room

The DLC hides three arenas, a Plato story, and two company presidents

The CEO boss fight

Some sidequests are effectively secret lore rooms

Treasure Hunt at the Castle opens the Forest King’s graveyard

Heritage of the Past is one of the game’s strongest links to the first NieR

Gathering Keepsakes revisits the Lunar Tear location

The hacking arcade is an unlock many players forget exists

A handful of crossover and series references are hidden in the equipment and scenery

Kainé’s shack and Lunar Tears

Engine Blade

Cypress Stick

The weapon-story system itself

One famous “secret” that is not in the game: the Copied City church

A practical “I want to see everything weird” route

Compact missability checklist

Sources

Endings, quests, and progression

Emil, Lunar Tears, and hidden areas

Weapons, Pods, and optional combat

Trophies, cheat code, and debugging

DLC and later-discovered secrets