From the Main Menu choose "New Game," then "Empty." This will begin the game and fade in with you facing a wall with "WAKE UP ALEX" painted on it.
Prison Cell
If you turn 90 degrees to your right you'll see the cell door, and to the right of it is a panel with two rows of five buttons.
Move the crosshair over the jigsaw piece on the two rows of buttons and then press 
to interact with the puzzle (I won't explicitly state this every time, but when I say to interact with something, this is the method you should use. Interaction points have a double circle over them if they're something to pick up, or a double circle with two jigsaw pieces if they're a puzzle).
The game will zoom into the panel and give you control of a cursor. Using the left stick to move the cursor, and to interact with the buttons, press the buttons in the following order;
You will hear a very faint beep after each button press, but they will not light up, so it's important to keep track of where you're up to in the sequence:
X 2 1 5 X
X X 4 3 X
This will open the cell door allowing you access to the Cell Block and unlock
Cell Block
Once outside your cell, if you turn 90 degrees to your left you will see the Guard Booth. We need to go to the door of this room, which is on the right wall as you're looking at it.
The keypad to the right of the door is the next puzzle, the code to gain entry to the Guard Booth is 4415525. This will appear in the little box above the number keys as you're typing it.
Once you've done this, the door to the guard booth will open and unlock
CellsYou escaped from the Cells!
Guard Booth
At the far end of the Guard booth, you will see four coloured buttons on the left-hand side (beneath the screens with numbers on them).
To get the Sedation Room Keycard, you need to press the buttons in the following order:
Blue, Blue, Blue, Orange, Orange, Blue, Blue, Blue, Orange, Orange.
Again, you will get no visual confirmation of button presses, just a clicking noise, so if you think you've gone wrong, use the reset button at the top of the screen.
Once you've got the sequence correct, the Keycard will pop up from the top of the monitors and it will unlock
Interact with the keycard to put it in your inventory.
In this screenshot, the door on the left is the Sedation Room, and on the right is the Investigation Room.
Head out of the Guard Booth, then double back so you're going towards those two doors.
We've just picked up the Keycard for the Sedation Room, so interact with the card reader to the right of the door to gain access to the Sedation Room
Sedation Room
On the wall immediately to the left of the door to this room, you will find four clocks with "HOURS // MINUTES" written above them.
The Start time needs to be set to 9 on the hours and 15 on the minutes.
The End time needs to be set to 6 on the hours and 15 on the minutes.
For those of you not familiar with an analogue clock, it should look like this:
This will open a drawer in the cabinet underneath the clocks. Interacting with the lever in the drawer will put it in your inventory. I found it can be a bit fiddly to get the interaction zone to show up on this for some reason, so if you're having trouble getting it to show up, try backing away from the drawer and re-approaching it.
Once you have the lever, you need to go to the far end of this room, to see a door on the left side wall.
To the right of this door is a circle of eight levers with a space for another.
Interacting with the circle will automatically put the lever from your inventory in the space.
The levers are "on" when the yellow tab is in the centre of the circle.
Going clockwise, counting the lever the yellow arrow is pointing to as "1," you need to turn on positions 1, 2, 4, 6 & 8.
Solving this will open the door you're standing next to and unlock
Proceeding through the newly-opened door, your character will have some choice observations about the room you're entering.
As you are standing in the doorway of this room, look to the right of the central table and you should see a cabinet with a case on it that has an open lid.
Inside the case, you'll find a yellow grid and five green balls.
To solve this puzzle, you need to put balls in the following spaces:
Row 1 - Column 1,
Row 2 - Columns 3, 5 & 6,
Row 3 - Column 5.
Once the balls are all in place, the drawer at the top of the cabinet will open revealing the blue keycard and it will unlock
Interact with the keycard to put it in your inventory.
Now that we have the keycard, we need to go all the way back out to the Cell Block and open the Investigation Room. It's to the left as you exit the Sedation room, past the clock puzzle.
Once again, the card reader is to the right of the door, and interacting with it will automatically use the blue keycard we picked up earlier and open the door.
Investigation Room
Slightly to the right as you step into the room is the first puzzle. It's got several red lights on it and a blue tray of pins in front of it.
You need to put as many pins in a row/column as there are red lights at the right or underneath it.
Row 1 - Columns 1 & 2
Row 2 - Columns 1, 2 & 3
Row 3 - Column 2
When you've completed this puzzle, the clue for the test tube puzzle "Paper with circles" will pop out of the slot on the right of the machine. For some reason, you cannot start the test tubes puzzle without this paper.
Once you have the paper with circles, if you turn 90 degrees to your right you will see a container with test tubes on a bench (it's the one with red, yellow, green, blue & grey things sticking out of the top of it).
Interacting with the puzzle will place the paper in the dotted outline and allow you to move the test tubes.
Once they're all placed correctly you will have three full rows that will be like this:
Row 1 - Blue, Green, Yellow, Blue, Green
Row 2 - Yellow, Blue, Red, Grey, Yellow
Row 3 - Red, Yellow, Green, Blue, Grey
Once solved, the drawer beneath the tube rack will open, giving you a red lever.
It's part of the fume cupboard that is on the wall to your left, so head there and interact with the bottom (puzzle) hotspot on the front of the cabinet to place the red lever you just acquired.
Interacting with a tap will turn it 90 degrees anti-clockwise,
this is how many times you need to interact with each tap
Group 1 - 1, 0, 0
Group 2 - 3, 3, 1
Group 3 - 1, 3, 0
to get this configuration.
Once you've got this correct, the front of the cabinet will slide up so you will be able to grab the red keycard from inside and it will unlock
The red keycard allows access to the Corridor. It's through the double doors that are opposite the Guard Booth door.
Head over there and interact with the card reader to the right of the doors to open them (only one of the doors opens, but it's all the invite you should need).
Corridor
Directly ahead of you, as you go through the door into the corridor, there is a combination lock on a cell door (it's got a door and a light bulb drawn in white right next to it).
The combination to open this door (from top to bottom) is 4696 - interacting with a dial will cause it to increase by one each time.
In the next room is a mini filing cabinet safe on the desk. Go around behind the desk and use the code 1212 to open it, giving you the purple keycard.
With this keycard in your inventory, head to the keycard reader to the left of the doors with 1352 written on them.
Interacting with the reader will use the keycard, but you still need to put the code 1641 into the keypad. It's another one that quietly beeps to let you know a key press has registered, so listen carefully.
Opening the doors will also unlock
Once the doors open, head through into the waiting room, and interact with the keypad underneath the Director's Office sign.
The code to get the door open is DRKAPANDJI.
Opening the door will unlock
Director's Office
As you enter this room, there is a shelf with binders on it opposite you, and at the bottom of the shelf is a safe.
The code to this safe is 145.
Collect the triangle ball from the safe, then turn around to look at the desk. You should see a triangular-shaped board on the desk that you can interact with.
To solve this puzzle, you must fill the left side with yellow balls, the bottom space with a red (pink?) ball, and the right side with a green ball.
Completing the puzzle will cause a picture behind you to slide to the side, revealing another puzzle.
The solution to this puzzle is C5C9V8, this is another one where you need to interact with each dial for it to move one position, so some dials take more than one interaction.
Once this is solved, you'll get a cutscene of another painting moving up, and a cabinet on a wall swinging open. Triggering this will unlock
Head out of the room and you should see a door with an Exit sign above it and a (newly-opened) cabinet to the left of it.
Head over to the door and interact with the cabinet.
The solution to this final puzzle is NO.
Solving this will open the door and unlock the final achievement
EscapeYou escaped from the Facility!
To finish the game and see the end scene, all that you need to do from here is walk through the newly opened door and to the end of the "corridor."
Congrats on your latest 1,000 G and thanks for following along!