NieR: Automata – Hidden Machines, Lost YoRHa Units, Ghost Data, Forbidden Endings, and the Secrets Buried in the Ruins of Humanity

NieR: Automata is a story of cycles — birth, death, recursion, repetition.
But beneath its stylish combat lies a vast network of secrets connecting multiple timelines, generations of androids, ancient experiments, and the cosmic tragedy of Project YoRHa.
Some of these truths completely reframe the meaning of 2B, 9S, and A2’s journey.

This article uncovers the deepest, most philosophical, and most emotionally devastating secrets in the NieR universe.

Hidden Quest – “The Memory of Unit 2E”

A secret storyline revealing 2B’s true designation — far earlier than the main game allows.

How to Trigger It:

1. Finish the first playthrough (Route A).

2. Start Route B and gain access to 9S’s hacking.

3. Hack the YoRHa server in the Bunker three times during downtime.

On the third hack, 9S discovers an encrypted file titled:
“CLASSIFIED – Unit 2E Termination Protocol”

Reading it triggers an unlisted quest where you track remnants of past 2E units across abandoned YoRHa execution sites.
You find message fragments like:
“I don’t want to kill him… not again.”

Finishing the quest gives the Executioner’s Flower, a passive chip increasing attack power when fighting alongside 9S.

This quest reveals the emotional cost of 2B’s repeated resets of 9S.

Hidden Boss – The Broken God of the Desert

A failed, god-like machine trying to reassemble its shattered consciousness.

How to Encounter It:

1. In Route C, after defeating Adam & Eve

2. Return to the Desert Zone at night

3. Approach the collapsed statue in the deepest pit

The sand shakes, and a colossal, half-formed machine rises — The Broken God.
It attacks by:

• Launching philosophical text projectiles

• Splitting into multiple “identity fragments”

• Pulling you into a hacking arena containing distorted biblical passages

Defeating it drops the God Fragment Core, used to craft a weapon enhancement tied to Emil’s backstory.

Its death cry:
“A god… is only the idea of god…”
A direct reference to machines developing metaphysical thought.

Hidden Area – The Shrine of the First Machine

A mysterious location showing the first machine-lifeform ever built.

How to Access It:

1. Complete all Pascal quests

2. Refuse to kill his children

3. Return to his village at dusk

A glowing firefly-like drone guides you to a hidden cave behind the waterfall.
Inside:

• A small, rusted machine infant

• Murals showing machines learning emotions

• Logs calling it “Prototype M-001”

Interacting with the infant grants the Lamentation Data, unlocking new lore in the Archives about how machines gained consciousness through copying human neural pathways.

Hidden Mechanic – The YoRHa Soul Weight System

NieR tracks more than XP and chips — it secretly tracks emotional burden.

Unlisted Behavior:

• After major story deaths, 2B and 9S move slightly slower for ~30 minutes

• Their idle animations linger longer

• 2B’s pod occasionally says “Unit seems stressed”

• During Route C, A2’s dodge becomes sharper if you have low emotional burden

• High burden causes your pod voice to distort slightly

This hidden system reinforces the themes of grief and memory.

Hidden Weapon – The Sword of Quiet Rain

A blade tied to a timeline crossover with NieR Replicant.

How to Obtain It:

1. Collect all 40 weapon stories

2. Visit the Amusement Park theater

3. Play the music box near the stage for one minute

A ghostly figure appears — Yonah’s silhouette — leaving behind the Sword of Quiet Rain.
Its passive ability:

• Gains attack power the more sad music tracks you’ve listened to
  The description subtly references the tragedy of the White Chlorination Syndrome.

Hidden Quest – “The Three Ghosts of City Ruins”

A quest about memories trapped in a recursive loop.

How to Trigger It:

1. Visit the skyscraper ruins between 2–3 AM (in-game)

2. Three android “ghosts” appear, whispering the line:
   “We died here. We die here. We will die here.”

Following them through three collapsed towers reveals:

• Their original black-boxes

• A memory recording showing they were YoRHa prototypes marked for disposal

Reward: Black Box Echo Chip, boosting Pod cooldown and unlocking special Pod dialogue about regret.

Hidden Enemy – The Eternal Child Machine

A machine that never grows, never fights, only watches.

Where to Find It:

1. Visit the Flooded City after Route C

2. Swim to the farthest broken tower

3. A small machine child sits, staring at the ocean

If attacked, it only says:
“Don’t…”

If left alone for 10 minutes, it stands and bows.
Pods analyze it as a machine “attempting to understand serenity.”

Hidden Area – The Fallen Bunker Garden

Part of the Bunker that was scorched away before the attack.

How to Access It:

1. During Route B, hack the Maintenance Core

2. Access “Directory 0xAB – Sealed Zone”

3. Teleport to a forgotten garden filled with artificial flowers

This garden contains:

• Logs written by 2B

• Messages confessing her pain about killing 9S

• A single pod flower labeled “Hope”

One of the most heartbreaking hidden spaces in the entire game.

Hidden Ending Variant – “Ending Σ (Sigma): The One Who Remembers Love)”

A secret epilogue reflecting ultimate compassion.

How to Unlock It:

1. Restore every weapon story

2. Collect all Pod programs

3. Spare every non-hostile machine

4. Complete all ending routes A–E without deleting save data

5. Return to the desert crater one final time

2B, 9S, and A2 appear in ghost-like projections.
A soft voice says:
“The cycle ends when someone remembers love.”

A butterfly lands on the Pod.
Screen fades to white.

One of the rarest endings in the game.

Bonus Tip – The 2B Smile Glitch (Intentional)

If you leave 2B idle in the sun for 90 seconds, she will subtly smile.
The developers later confirmed this wasn’t a glitch…
but a hint she always had emotions she wasn’t allowed to express.

Why NieR: Automata’s Secrets Make It a Masterpiece

NieR’s secrets aren’t just Easter eggs — they are emotional knives.
Every hidden quest explores identity, death, recursion, trauma, the cost of memory, and the beauty of fragile lifeforms trying to understand meaning.
The deeper you search, the more human the machines become — and the more machine-like the androids appear.

Because in NieR: Automata…
understanding truth is the same as breaking.