This guide is barebones. It's intended to allow self-exploration, but prevent FOMO by allowing players to check what they might have missed in different areas of the game, as well as provide solutions or remove doubts on which puzzle or locked door should be done next.

All names were standardized in the guide (I hope), so you can CTRL+F for wanted items:

• Inventory Expansion
  
• Upgrade Item
  
• Pistol Bullets
  
• Shotgun Shells
  
• Machine Gun Bullets
  
• Revolver Bullets
  
• Gauze
  
• Adhesive Plaster
  
• Simple Bandage
  
• Small Alcohol
  
• Strong Bandage

As for gameplay type, the guide is intended for completionists (Want to collect all collectibles and resources), but I provide two ways of playing following the guide.
Vanilla: You follow the dev's intended game path and only solve the puzzles when you should
Speedrun: You "magically know" some codes and get hold of items you shouldn't be getting so soon in the game

Regardless of the above, ALL solutions are shown in this guide. If you don't want spoilers, don't read too much ahead. If you're the opposite and want spoilers and to not be caught with your pants down, I warn before a particular complicated scene, bossfight or long/difficult section is ahead.

» Cell
Grab Metal Key
Read note
Exit cell

» Prison
Go to desk
Grab Key IV & Diary
Read 2 notes
Open cell IV

» Cell IV
Place diary on bricks
Exit cell

» Prison
Press lever next to gate

» Corridor
Cutscene, run, turn right, cutscene

» Lobby
Press bell, cutscene
Grab Room 610 Key
Open doors down the hallway to the right
At the right of the doors, table, read 5 notes
Elevator, cutscene

» Room 610
Desk, grab Inventory Expansion (1/13), Gauze
Small desk, read note, read laptop
Grab Pocket Watch, Metal Object
Inspect Metal Object, numbers = combination of suitcase on floor
Open suitcase on floor, grab Bathroom Key
Read bulletin board
Grab Jonisvaldo (Paper) lower right corner
Open bathroom, grab Camera Lens from shelve
Open suitcase on floor, read note
Wardrobe, open safe with 37251, grab Camera Body
Open inventory, combine Camera Lens + Camera Body
Equip camera, interact with writing above bed
Enter bathroom, cutscene
Equip camera, desk, interact with photo
Interact with box on chair
Chest at foot of bed, grab Adhesive Plaster
Open inventory, combine Adhesive Plaster + Gauze = Bandage
Exit room

» 6th floor left wing corridor
Cabinet, grab Inventory Expansion (2/13)
Read note

» Room 611
Equip camera, go to bathroom
Exit to corridor through hole

» 6th floor left wing corridor
Room 608, grab Key of a drawer
Go back, girl will spawn, DO NOT GET CLOSE, wait for de-spawn
Return to cabinet on corridor
Open locked drawer, grab Room 608 Key

» Room 608
Equip camera
Open safe with 6749, grab Inventory Expansion (3/13), Bandage

» Room 606
Open safe (no code), grab Room 606 key

» 6th floor center
Open gate, read note

» 6th floor right wing corridor
Mid-way "lounge", right side, grab Gauze
End of corridor cabinet, grab Inventory Expansion (4/13), Adhesive Plaster

» 6th floor center
Go down the stairs, pick Gauze from small table, cutscene

» 5th floor center
Open gate, drawers to the left, read 4 notes
Speedrun: Counting from bottom left to top right, open drawers A4, A10, B2, D3, E1
Speedrun: Leave Metal Gear in the drawer, for now
Go through hole, left, open box, grab Red Card, read note
Go back, pick up phone, cutscene

» 6th floor center
Use Red Card + 67352
Vanilla: Equip camera, look at picture at the right = Solution of 5th floor drawers
Down the corridor, right gate, downstairs
Lockers, grab Flashlight, read note
Open box with 164 871, grab Blue Corridor Bathroom Key, Pistol Bullets
Go downstairs, grab Upgrade Item (1/52), Inventory Expansion (5/13)
Speedrun: Go upstairs twice (back to 6th floor center), use Red Card + 775492, grab Upgrade Item (13/52). Discard Red Card

» 5th floor center
Open WC Door

» 5th floor right wing corridor
Read note on elevator

» 5th floor service room
Dump Metal Object, Red Card, Metal Gear, take Pistol Bullets in the Item Box
Equip camera, open box, grab Room 603 Key, Electronic Circuit
Save game

» 5th floor right wing corridor
After ducking under cabinet, girl will spawn, wait for de-spawn
Left, drawer, grab Adhesive Plaster
End of corridor, cabinet, read note

» Room 603
Open box on bed, take Cassette Recorder, Cassette Tape
Open inventory, combine the above, listen
Bedside table, grab Gauze, Pistol Bullets
Desk, open box with 30 Right, 10 Left, 5 Right, take Allen Key

» 5th floor center
Use Allen Key on elevator panel, solve puzzle
Enter elevator, take 7th Floor Button, install on elevator

» 7th floor center
Interact with door to the right
Go down the stairs, grab Upgrade Item (2/52)
Drawers, grab Pistol Bullets

» 9th floor
Open box, read note, grab Pistol Bullets, grab 1911 .45 Pistol
Shoot 1 Claw monster
Read note, go to right side, grab Mezzanine 1 Key
Go to left side, grab Upgrade Item (3/52), grab White Queen Chess Piece

» 7th floor center
Place chess piece on the board
Move E2 to E4, then F1 to C4, then D1 to F3, then F3 to F7
Grab Pistol Bullets, 6th Floor Service Room Key
Leave Metal Gear, for now

» 5th floor left wing
Shoot/be attacked by 4 Mutant bugs
Grab Gauze at the left, read note
Go through hole

» Room 508
Grab Upgrade Item (4/52)
Right bedside table, grab Inventory Expansion (6/13), Pistol Bullets
Left beside table, grab MEMORY (1/20) The Origin of spaces

» 6th floor center
I recommend you save on 5th floor before this section
Kill 2 Claw Mutants

» 6th floor service room
Equip camera, open box, grab Pistol Bullets
Drawers, grab Pistol Bullets, Upgrade Item (5/52)
Suitcase, grab Simple Bandage, Pistol Bullets
Grab 1st Floor Button from panel
Exit, cutscene
Stand by the left side of corridor, so that Aquiles walks along left side. Shoot him until he flinches/kneels and run past him OR run directly, be grabbed and then you can run downstairs, enter elevator, apply 1st Floor Button and finish this section

» Bedroom
Read note
Wardrobe, grab MEMORY (2/20) Pocket Watch
Go downstairs

» Living room
Right of stairs, read note

» Bathroom
Grab Kitchen Door Key

» Kitchen
Grab Office Key
Go upstairs

» Office
Open box, grab 4 items, combine (by numerical order) in inventory
Read notebook
Go downstairs

» Living room
Open gun cabinet, grab Metal Piece 4
Combine Modular Key + Metal Piece 4
Go upstairs

» Bedroom
Open box, grab Sphere
Go downstairs, save your game
Exit house through door next to Bathroom

» 1st Floor left wing
Go left, desk after blocked stairs, grab Adhesive Plaster, Gauze
Keep walking forward, 3rd desk, grab Pistol Bullets, Inventory Expansion (7/13)
NOTICE THE PRAYING NUN PAINTING TO THE LEFT OF THIS DESK. Interact with it. You DON'T need to pick the Encrypted Document yet.
Move down the corridor to the other side
Shoot 1 Claw Mutant
NOTICE THE GEARS PAINTING, grab Metal Gear from bottom left corner
Table in the middle, grab Pistol Bullets
Second table, read note, grab Pistol Bullets, Small Alcohol
You can combine Simple Bandage + Small Alcohol = Strong Bandage

» Ground Floor
To the right of stairs, grab Adhesive Plaster, Pistol Bullets from tables near pillars
Directly ahead of stairs, grab Upgrade Item (6/52), examine the items on the table
To the left of stairs, read note, grab Pistol Bullets near Save Clock
Go to ringing phone, grab Library Key, answer phone, cutscene

» 1st Floor left wing
Open Library doors on both sides, discard the key

» Library
Starting from the side with the Praying Nun painting
Bookcase to the right, grab Small Alcohol
Read note on table
Speedrun: Equip camera, open safe with 012345679, grab 3 Metal Keys
Speedrun: Left of our Item Box, open locked drawer with 25 Right, 15 Left, 20 Right, grab Key to a Safe, interact with picture
On the other side of the room, on the desk, grab Pistol Bullets
On cabinet, grab Shotgun Shells
Open floor safe with 32 Right, 16 Left, 4 Right
Read note, grab Handle, Metal Cube
Speedrun: Open locked door on safe with Key to a Safe, grab MEMORY (11/20) - Earring, read note
Open inventory, press use on Metal Cube
Start with inner-most circle, rotate until upright, then outer-most circle
Combine Handle + Metal Cube
Flip switch number 3, 6 and 9
Combine Ornate Key with the Metal Pieces
Open box on table, grab Meeting Room 2 Key
Equip camera, look at bookshelve and grab The 3 Musketeers Book
Drop in Items Box the 3 Musketeers Book, Metal Gear, Cassette Recorder
I recommend a save

» 1st Floor right wing
Run to area at the right of the elevator (when exiting elevator)
When entering, drawer to the right, grab Pistol bullets
Foward, blue table, grab Pistol Bullets
Move down the corridor, shoot/get attacked by 3 Mutant Bugs
Shoot 1 Claw Mutant
Girl will spawn, wait for despawn
Behind where girl spawned, desk, grab Pistol Bullets

» Meeting Room 2
Grab Upgrade Item (7/52), Pistol Bullets, Cassette Tape, 3rd Floor Button

» 1st Floor right wing
Go back, shoot 1 Claw Mutant on infested area
Shoot 2 Claw Mutants in front of elevator

» 3rd Floor center
Grab Pistol Bullets twice
Equip camera, grab Adhesive Plaster
Go upstairs, grab Upgrade Item (8/52), Shotgun Shells
Enter gated room, cutscene
Grab Shotgun, Inventory Expansion (8/13), Conference Room Key, MEMORY (3/20) - Military ID (Dog Tags), Pistol Bullets, Simple Bandage, Shotgun Shells
Equip camera, grab Pistol Bullets twice

» 1st Floor right wing
SAVE GAME, boss fight incoming

» Conference Room
Left of box in floor, grab Pistol Bullets
Open box, grab Pistol Bullets, Screen, read note
Use Metal Cube in your inventory
Press buttons on this order: Top left corner, bottom right corner, top right corner, middle in the bottom, middle in the left, bottom left corner
Combine Modular Key + Metal Piece 3
Exit room, cutscene
BOSS FIGHT, do not run to other side of corridor else Claw Mutants will spawn. You can find Shotgun Shells (x1?) and Pistol Bullets (x3?) on the area in front of Conference Room door

» 7th Floor right wing corridor
Mid-way, table, read note
Drawer, grab Strong Bandage, Pistol Bullets
Interact with plaque above drawer
Interact with pictures by this order 1, 5, 3, 2, 4
End of corridor, grab Upgrade Item (9/52), Pistol Bullets, Cassette Tape

» 7th Floor left wing corridor
Mid-way, drawer, grab Machine Gun Bullets
Interact with plaque above drawer
Interact with pictures by this order 3, 4, 2, 5, 1
Equip camera, end of corridor, grab Crowbar, Shotgun Shells, Upgrade Item (10/52)

» Room 711
Closet, grab Upgrade Item (11/52), Pistol Bullets, MEMORY (4/20) - Ring

» 7th Floor center
Open previously hidden door
Desk, read note, open box, grab Blue Card, grab Shotgun Shells from drawers
Read computer
Bookcase, grab Upgrade Item (12/52), Inventory Expansion (9/13)
Exit room, go to Chess Board in front of Elevator, Grab Metal Gear
Go to elevator, stop in 6th floor, use Crowbar and discard it

» 6th Floor center
Shoot 1 Claw Mutant at the left just after going through the gate you unlocked with Red Card a while ago
Vanilla: Use Red Card + 775492 on locked door. You can discard Red Card now. Grab Upgrade Item (13/52)
Speedrun: Unlock box with 3 Metal Keys, grab Upgrade Item (36/52)

» 5th Floor center
Grab Metal Gear from the drawers in the central room
Grab Metal Gear, The 3 Musketeers Book from Item Box
Vanilla: Grab Red Card from Item Box
Save your game, why not
Go to center, equip camera, duck under things to reach gate
Use Blue Card + 645820. Discard Blue Card
At your right, picture on wall, interact with it
Plaque on wall, place the 3 Metal Gears
Interact with left gear, point arrow to T
Interact with middle gear, point arrow to F
Interact with right gear, point arrow to M
Black cabinet, unlock safe with 19 Right, 17 Left, 24 Right
Grab from safe Inventory Expansion (10/13), Upgrade Item (14/52), Pistol Bullets, Shotgun Shells
Table behind you, grab Pistol Bullets
Desk, grab Pistol Bullets, equip camera, grab Shotgun Shells
Equip camera, new bookshelve, place The 3 Musketeers Book
Rearrange books on this order: 1, 2, Triangle, 3, 5, 6, 7
Hidden room, grab Upgrade item (15/52)
If screen says TFM, interact with plaque as described above
If screen says FOBIA, interact with it and write YHUBT
Exit to backrooms, go upstairs

» 6th Floor backrooms
Shoot 3 Mutant Bugs
Grab Pistol Bullets, Metal Gate of 6th Floor Key, Upgrade Item (16/52)
Open gate with new key
Go downstairs, I recommend a save now

» 4th Floor backrooms
Shoot 1 Claw Mutant on the hallway
Grab Shotgun Shells, Pistol Bullets
Shoot 1 Claw Mutant on the mid-section of the 4th Floor
Grab Pistol Bullets on desk next to doorway leading to 4th Floor center
Exit to 4th Floor center, cutscene

» 4th Floor center
Go upstairs, grab Upgrade Item (17/52), Shotgun Shells
Go down the ramp on the left wing

» Room 210 & 208
Item Box to your left, if you need
Equip camera, go through hole in bathroom
Look into bathtub, grab Upgrade Item (18/52)
Grab Machine Gun Bullets

» 2nd Floor center
Shoot 2 Claw Mutants

» 2nd Floor right wing
Shoot 2 Mutant Bugs

» Room 300
Closet, grab MEMORY (5/20) - Pendant
Bathroom, grab Upgrade Item (19/52)

» Room 302
Grab Pistol Bullets, Upgrade Item (20/52), Machine Gun MP-28

» Room 303
Bed, grab Shotgun Shells, Machine Gun Bullets
Desk, grab Pistol Bullets x2
Closet, read plaque, unlock box with SIMAO
Grab Weird Piece of Metal, Room 404 Key
Bathroom, grab Machine Gun Bullets, Upgrade Item (21/52) inside toilet
Exit room, look to your right, shoot 1 Claw Mutant
Running sequence incoming!

» 2nd/3rd Floor
Running sequence incoming! Read before proceeding!
Cutscene, Aquiles will spawn, run towards the center, another cutscene
The game wants you to go to 1st Floor, but I have better plans
You will instead shoot Aquiles so he flinches/kneels, shoot Claw Mutant behind him and run through Room 208/210 with your camera
Aquiles cannot follow you through camera-only passages
Game will still be playing running music, but you can chill

» Room 404
Grab Upgrade Item (22/52), Pliers, MEMORY (6/20) - Magic Cube
Go back through room 208/210

» 2nd Floor center
Shoot 1 Claw Mutant (If you didn't kill it on running sequence)

» 1st Floor center
Shoot 1 Claw Mutant in front of elevator
Two more Claw Mutants (maybe 3?) in the other side of the mezzanine/balcony overlooking Ground Floor

» 7th Floor left wing
Shoot 3 Mutant Bugs

» Room 709
Equip camera, grab Metal Rod, use it on articulated stairs above you
Now let's get rid of Pliers, Metal Rod, they occupy too much space. Make sure to leave
Speedrun: Also 3 Metal Keys

» 6th Floor center
Remember that area with gates and articulated stairs? Go there
Enter gate at right, look up, use Metal Rod
Go downstairs to 4th Floor center, across to other side
Use Metal Rod on ceiling above, access 5th Floor center
Use Metal Rod on ceiling above, access 6th Floor center
Grab Shotgun Shells, Pistol Bullets, Upgrade Item (23/52)
Use Metal Rod on ceiling above, you can now discard the Metal Rod
Grab Revolver from the wall, go upstairs
On 7th Floor, grab Upgrade Item (24/52) and go down the other stairs to leave the area

» Room 604
Grab Strong bandage
Desk, grab MEMORY (7/20) - Stethoscope, Adhesive Plaster, Gauze
Cabinet, open safe with 251, grab Locker Key
Equip camera, open locked locker, grab Upgrade Item (25/52)
Equip camera, go to bathtub, grab Shotgun Shells
Remove camera, read note from plant
Go downstairs

» Room 508
Speedrun: Open box with 3 Metal Keys, grab Upgrade Item (37/52), Gear with Numbers

» 5th Floor center
Equip camera, duck to access backrooms area, use pliers on locked door, grab Upgrade Item (26/52), Strong Bandage
Go back, and upstairs, use elevator to 5th floor

» Room 501
Equip camera, use pliers. After opening it, you can discard the pliers
No camera, cabinet, grab Pistol Bullets, Shotgun Shells
No camera, table, grab Upgrade Item (27/52), Small Alcohol
Camera, open briefcase with 483, grab Upgrade Item (28/52)
Speedrun: Open box with 3 Metal Keys. You can now discard the keys. Grab Upgrade Item (38/52)

» Room 709
Equip camera, move up the articulated stairs

» Backstage on 8th Floor
Move towards save clock, doors to the left
Grab Small Alcohol from one room
Grab Machine Gun Bullets and White Card from other room
Near the gate, red sofa, grab Shotgun Shells
Organize your inventory, get ready for a Boss fight
Save your game
Open door with White Card + 9568, cutscene

» Piano room
Bossfight
Next to a big table, grab Simple Bandage, Machine Gun Bullets, Shotgun Shells and Pistol Bullets x2
On stage, grab Strong Bandage, Machine Gun Bullets, Shotgun Shells x2 and Pistol Bullets x2
Open door with White Card + 5527

» Backstage on 8th Floor
Interact with baggage cart to open gate and maybe save your game
Go up the articulated stairs

» Backstage on 9th Floor
At the top of stage on other side, grab MEMORY (8/20) - Sheet of Music
Grab Cassette Tape, Machine Gun Bullets, Backstage Key, 8th Floor Button
Use key on both gates in this area. You can discard the key now
Go out to the 9th Floor center, down the stairs, shoot one Claw Monster, enter the elevator, use 8th Floor Button

» 8th Floor center
To your left, use White Card + 1102. You can discard the White Card now.
Read note to the right of now-open door
Go up the stairs in front of statue
Grab Handle and read note at left of the door
Hug doors, look right, walk along the wall, read note on top of the lamp
Go behind reception desk, use Handle on cash register, grab Mezzanine 2 Key
Look to left, white cabinet, read note
Look left, black cabinet, take Adhesive Plaster
Open safe with 1649, grab Machine Gun Bullets, Revolver Bullets

» 9th Floor
Go to right wing, shoot one Claw Monster
Open door
Puzzle, align the symbols. Place top left cog "+" sign pointing to center cog, align all other cogs accordingly
Grab Reception Key
Speedrun: Take all three Gears with Numbers with you

» 1st Floor
Shoot Claw Mutant from walkway ahead of you
To your right, on infested area, new room is open

» Meeting Room 1
Grab Pistol Bullets, Shotgun Shells
Look at frame next to safe, rotate coins until line is at the bottom
Equip camera, repeat for remaining coins
READ! On safe, grab Upgrade Item (29/52). You DON'T NEED the Coin with Combination! Leave it for extra inventory space. This is the combination for locked (Vanilla) or unlocked (Speedrun) drawer in Library Room

» 1st Floor right wing
Go around, shoot 3 Claw Mutants near the stairs to Ground Floor
Speedrun: Remember the Praying Nun painting which had the Encrypted Document behind, near Library? Go grab it

» Ground Floor
Speedrun: If you have them with you, place the 3 Gear with Numbers on the Enigma Puzzle right in front of the stairs you just came from. Use the Encrypted Document on it. Code will probably be 271, but it might also be 303.
Save your game
Use reception key

» Reception
Grab Simple Bandage, read note on reception desk
Equip camera, go to right side room
Grab Upgrade Item (30/52), Machine Gun Bullets
Open box, grab Administration Key, Circuit
Equip camera, leave room, go to other room
Grab Pistol bullets, Shotgun Shells, MEMORY (9/20) - MP3 Player
Organize inventory with Item Box next to you, why not
Pick up the phone, cutscene
Run sequence again!

» Ground floor
Run sequence again! You have enemies across your path
Shoot/run by Claw Mutant on stairs behind Aquiles
Go up the stairs

» 1st Floor right wing
Shoot/run by 1 (or more?) Claw Mutants
Go up the stairs to 2nd floor

» 2nd Floor
Shoot 1 Claw Mutant on left wing, go to room 208
Equip camera, step into room 210
Running ended

» 3rd Floor center
Fix elevator

» 8th Floor center
Shoot chalice from statue, grab it from the floor
Unlock Administration Room

» Administration Room
On table, grab Shotgun Shells, Machine Gun Bullets, read book
Cabinet to the right, grab Pistol Bullets
On desk, interact with monitors and picture
On desk, grab Upgrade Item (31/52), Pistol Bullets and Machine Gun Ammo
Above fireplace, place Chalice, small cutscene
Open safe with 35 Right, 5 Left, 30 right
Grab Piano Key, Small Gear, read note
Combine Small Gear + Metal Cube, solve puzzle
You can now discard the Metal Cube
Combine Metal Piece 4 + Modular Key
Open box on table, grab Upgrade Item (32/52)
Open box with 784, grab Coin
Fireplace, place Coin on Lion's Head
Save, exit room

» 8th Floor center
Newly exposed area, grab Upgrade Item (33/52), read note

» 6th Floor left wing
Enter room 606, pass to room 608
Shoot 1 Claw Mutant outside of room 608
Equip camera, step into room 611, exit and enter room 610

» Room 610
Grab MEMORY (10/20) - Stuffed Bunny (If it's not here yet, do the piano part and then come back)
Open box on chair, grab Upgrade Item (34/52)

» 1st Floor
Vanilla: Remember that coin we left in the safe in Meeting Room 1? You need that combination for the Library's locked drawer, inspect the coin but you don't need to take it with you

» Library
Equip camera, look and open locked box, grab Upgrade Item (35/52) and Pistol Bullets
Vanilla: Open the locked drawer with 25 Right, 15 Left, 20 Right, look at the picture, grab Key to a Safe
Vanilla: There's a safe on the floor we opened a while ago, go to it, open locked door on safe with Key to a Safe, grab MEMORY (11/20) - Earring, read note
Vanilla: Equip camera, find locked safe on top of table, open it with 012345679, grab 3 Metal Keys
Vanilla: Do CTRL+F for "3 Metal Keys" from the start of this guide to know where to use them
Vanilla: After gathering the 3 Gear with Numbers, CTRL+F for "Encrypted Document" and follow instructions

» 8th Floor Backstage
Shoot 2 Claw Mutants

» Piano Room
Shoot 1 Claw Mutant
Place Piano Key, play the piano
Select ONE number per line (I'm using "/" to facilitate reading)
Combination is: 0-1-1 / 2-3-5 / 8-1-3 / 2-1-3 / 4-5-5
Cutscene

» 8th Floor center
Shoot 2 Claw Mutants
Go down the new passageway, cutscene

» 7th Floor center
Here, grab Strong Bandage, Machine Gun Bullets and Black Card
Use Black Card + 400233, discard Black Card
Step into this office, open safe, grab Upgrade Item (39/52)
You should save your game before moving into next section

Intersection, go left, grab Sphere Fragment 1

Walk back, go right, follow image up to windmill, grab Sphere Fragment 2

Go back, building to left, center door
Open box, grab Administration Warehouse Key, cutscene, read note
Open door to left when leaving, grab Sphere Fragment 3

Exit, resume path, see door opening and closing?
Go there, read note, resume path
Reached gate, enter building to right, chapel to your left, follow path
Tree falls, enter building, open toolbox with 35 Right, 15 Left, 10 Right, grab Pliers
Closet, grab Sphere Fragment 4

Run back, open gate near chapel, enter right-most building, grab MEMORY (12/20) - Helmet
Exit, gate to your right, unlock, go to second building, read note
Exit, go back, walk towards a water tower until windmill falls
Unlock gate near water tower, and another gate at your right near a house
Go back, up & down the water tower, follow path, cutscene, grab Chapel Key
Chapel, cutscene, enter, cutscene, open box, grab Sphere Fragment 5

Exit, walk through other gate you opened previously but didn't go through
After windmill, enter house to right, cutscene, grab Sphere Fragment 6, read note, save game

Exit, follow rest of path, grab Sphere Fragment 7

To understand name references, refer to the map of the underground in 5 - Monitoring
Highlighted in red is what matters for this section
I added red lines indicating unmarked doors, added L and R and corridor level requirements to make it easier to understand my instructions


» Right Hallway Level 0
Grab Shotgun Shells, Pistol Bullets
Save game
Move cart, enter room at your left

» Lab 01
Shoot 1 Claw Mutant
Shoot 2 Mutant Bugs behind Claw Mutant
Bloody desk, grab Upgrade Item (40/52)
Cabinets, grab Pistol Bullets, Gauze
Interact with button to activate other door

» Left Hallway Level 0
Turn left, shoot 1 Mutant Bug
Equip camera, go through the right

» 2 - Data Processing
Shoot 1 Claw Mutant
Towards Item Box, grab Pistol Bullets, Simple Bandage
Read note, interact with computer, print and grab Card Level 1
Middle desk, read note
Red sofa, grab Gauze
Activate door, go back

» Right Hallway Level 1
Shoot 1 Claw Mutant in the distance, another around the right corner
Shoot 2 Mutant Bugs above the fence where last Claw Mutant was

» 5 - Monitoring
Look at the map at the left wall, familiarize yourself with the area
Lockers to left of map, grab Simple Bandage
Coffee machine to right of map, grab Small Alcohol
Crate at back, grab Shotgun Shells
Desk, interact with flatscreen monitors
Desk, grab Pistol Bullets, interact with CRT monitor
Generate access and grab USB Flash Drive from the computer tower
Activate door to left of computer

» 2 - Data Processing
Use USB Flash Drive in computer, generate code
Upon error, click "Yes", small cutscene
Go to unlocked door, on the back, grab Adhesive Plaster
Equip camera, grab Screwdriver

» 7 - Research
Middle, grab Shotgun Shells, read note
Drawers, grab Shotgun Shells, Adhesive Plaster, Small Alcohol
Left of crazy door, use screwdriver, solve puzzle
Inside new room, left, take Machine Gun Bullets, Shotgun Shells
Middle, take A19 Server

» 2 - Data Processing
Place A19 Server into slot, small cutscene
Interact with computer, print Card Level 2, discard Card Level 1
Grab Card Level 2 AND USB Flash Drive

» Left Hallway Level 2
Turn left, pull cart out so it doesn't block passageway between Labs

» 4 - Lab 02
Equip camera, open box in front of you, grab Revolver Bullets and Upgrade Item (41/52)
Go right, white cabinet, grab Upgrade Item (42/52) and Machine Gun Bullets
Cabinets under sink, grab Inventory Expansion (11/13)
Along the right, read note
Refrigerators, grab Shotgun Shells, Strong Bandage
Above the safe, interact with clocks: 8 - 11 - 4 - Pull lever
Cutscene
Open safe with 25 Right, 8 Left, 36 Right, grab Energy Redirector
Go inside windowed area, grab Energizer, Upgrade Item (43/52)
Go save your game

» 6 - Lab 03
READ!
Enter it through Lab 02, equip camera to pass the locked Lab 02 door
You have a Claw Mutant to your immediate left, rush in towards laying Claw Mutant to avoid being hit
Shoot said 2 Claw Mutants
Podium, read note
Equip camera, grab MEMORY (13/20) - Old Photo from podium, look right, grab Upgrade Item (44/52)
Use USB Flash Drive in computer, interact and generate Level 3 Access
Grab USB Flash Drive, go through next door
Running sequence incoming!

» 2 - Data Processing
Running sequence incoming!
Leave Lab 03, you are forced into a path
Aquiles spawns, run by him
In front of 5 - Monitoring, 2 Claw Mutants
Right after door to Right Hallway Level 0, 1 Claw Mutant
In front of 3 - Lab 01, 1 Claw Mutant
In Left Hallway Level 0, 1 Claw Mutant
You are safe when inside 2 - Data Processing
Place USB Flash Drive, print and grab Card Level 3, you can now discard Card Level 2
Item Box, keep at least 2 free slots in your inventory (Can drop Energizer, Energy Redirector)
Save your game, leave through other door, turn left

» 1 - Universal Transporter
Small room to the right, with 1 Claw Mutant inside
Drawers, grab Pistol Bullets
Open safe with 39 Right, 31 Left, 19 Right
Grab Performance Drink (Heals 100HP)
Go back towards Right Hallway Level 0, cutscene

» 8 - Staircase Underground 2
Go all the way down
Grab Upgrade Item (45/52)
Go up and through only open door

» Prison
Equip camera, take all 3 Cell Keys
Equip camera, desk, take Machine Gun Ammo, read file
Open all cells
VII: Grab Upgrade Item (46/52)
V: Grab MEMORY (14/20) - Rose
IV: Grab Diary from brick wall
Lockers, grab 1 or 2 items (Can't remember)

» Cells corridor
Move forward, enter room to right
Grab Shotgun Shells, Pistol Bullets
Take from Items Box the Metal Object, Energizer, Energy Redirector
Exit, move forward
Unfinished brick wall, equip camera, go through it and grab Inventory Expansion (12/13), Upgrade Item (47/52) and MEMORY (15/20) - Wrist Watch
Return, keep moving forward
Open door with Card Level 3 + 852369

» 1 - Universal Transporter (Lower level)
Grab Underground Transport (UT) Lab Access Card from Claw Mutant
Solve computer puzzle by clicking on the middle numbers: 499
Small cutscene
Go into Universal Transporter area, to the right
Use by order: Metal Object, Energy Redirector, Energizer
After cutscene, step into pod and RUN!
RUN, avoid obstacles, at the end, open door, grab MEMORY (16/20) - Fireplace Key

» Cells corridor
Shoot 2 Claw Mutants, one on corridor, one on doorway of Prison

» 8 - Staircase Underground 2
Go all the way up where Aquiles was hit, grab MEMORY (17/20) - Gas Mask
Go down and through one of the unused doors

» 10 - Underground 2
Save your game
It's a maze, but only two short dead ends, so it's easy by yourself
Explore ALL paths, but beware of the mutant bugs!
EXCLUDING the 3 rooms you'll come across, you have to:
Grab 4 Upgrade Items (48 to 51/52)
Shoot 7 Mutant Bugs
Activate 6 buttons

» Middle Room
Shoot 1 Claw Mutant
Grab Pistol Bullets, Gauze and Machine Gun Bullets
Equip camera, go to other section of the room, open freezer, WITH CAMERA grab Plasmodium Compound
Unequip camera, grab Simple Bandage
Open box, grab Revolver Bullets, Upgrade Item (52/52)

» Top Room
Shoot 2 Claw Mutants
Table across entrance, grab Pistol Bullets
Tray cart, grab Shotgun Shells
Microscope, grab MEMORY (18/20) - Petri Plate
Freezer, grab Batrachotoxin Compound

» Bottom Room
Shoot 2 Claw Mutants
First section of room, grab Adhesive Plaster, Machine Gun Bullets, read note
Second section of room, grab Shotgun Shells
On refrigerator, grab M Cells + Cycles
On the mixing machine, grab Gas 320 MTH Empty Tubes
Place all 4 items inside the machine
On panel, insert the values: 30, 20, 50
Press red button, take Gas 320 MTH Compound A, place second Gas 320 MTH Empty Tube
On panel, insert the values: 80, 15, 5
Press red button, take Gas 320 MTH Compound B
Exit this area and go back all the way upstairs

» 7 - Research
Right door, equip camera, grab Inventory Expansion (13/13), Gauze

» 5 - Monitoring
Interact with computer, press "Unlock Manually"
Go to now-open big gate room

» 11 - Underground 3
Left side, read note
Right side, grab MEMORY (19/20) - Glasses
Go downstairs, left side, grab absurd quantity of ammo + other supplies + one Gas Mask
Forward to the right, open rooms and apply Gas Compounds
Go back, organize your inventory
Prioritize using, by order: Revolver > Shotgun > SMG > Pistol
Take all your heals
Save your game
Bossfight

Cutscene
Grab Gas Mask, read note
Go left, grab MEMORY (20/20) - Ore
Cutscene after cutscene, and a WALK FORWARD tedious section later, you should select HAND to get two achievements instead of just one