Walkthrough Guide
This covers Mateuz's June 19th edit. It covers only the new content, which does not interfere with the flow of the original walkthrough...
Exploration
Spoiler
The gist of this update is that it ties in what I originally called "Legacy Rooms" into the subnet proper. There are also a few new legacy rooms. One of them can be found in the starting computer list, so let's go there first.
Lighthouse Dugouts, B
Spoiler
Code: 551 (Computer List, also found in 462)
You remember this room. The code to the other half of the chamber, which also hasn't changed, can be found on the left (THIS - 89). Another code, can be found attached to the theory.
New Codes:
Lighthouse Dugouts, A
Spoiler
Code: 462 (Result of equation "THIS - 89 in regards to room 551)
Uh... whoops. Understandably, there is not much to be found here, but a panel seems to have kept a steady grip. Unfortunately, it only points back to the other half of this room, above. Thankfully, a new code can be found on the left, if you hover over the block in the background. It does not seem to be otherwise readable.
New Codes:
Passageway
Spoiler
Code: 747 (551 - Theory)
If you've been reading the walkthroughs, you know this infamous room, which has an infinite hallway you can unlock with a key. The code is not actually there, though. Rather, the code can be found by mousing over the arrows just to the right of the teleporter, in letter form (where A=1, B=2, etc). There is no real explanation for how you find these letters, it's not really a good clue.
New Codes:
Ancient Zone
Spoiler
Code: 104 (462 - mouse over glyph)
A fair amount of new content has been added here in the update, including a bell with the number II on it and a panel far to the top-right of one of the screens. The codes below are listed in reverse just to speed the walkthrough up a bit.
New Codes:
Statue
Spoiler
Code: 452 (747 - right arrows)
The ending of Submachine 4, now with a panel stuck to the statue reading "DCCLXX", or...
New Codes:
Bonus Room
Spoiler
Code: 728 (747 - left arrows)
Submachine 4's Bonus Room. Here you can find updated versions of the pictures from the original bonus, along with new and old info. The old is a collection of Submachine 2 notes about Einstein, the long-forgotten cat, and the second is a code, EEB. Going with the A=1/B=2 code, that's...
New Codes:
The Ship
Spoiler
Code: 800 (104 - panel)
New information can be found in the ladder's former pipe, reading "WX=23 / WY=688"
Pit
Spoiler
Code: 002 (104 - bell platform)
This simple room contains a panel that reads "THIS + WY". We know WY from room 800, leading us to...
New Codes:
Tomb Trap
Spoiler
Code: 770 (452 - panel)
The Tomb Trap hasn't changed at all from Submachine 4, which is to say, it still contains the code for the Dome room in the shapes on the wall.
New Codes:
The Root
Spoiler
Code: 552 (728 - letter panel)
The Root has changed considerably, but the code you want is on a panel near the front, which reads "THIS - WX". We have WX thanks to room 800.
New Codes:
Looping Trap
Spoiler
Code: 690 (Result of equation "THIS + WY" in regards to Room 002)
This room from Submachine 4 contains the third green light, reading six, and a theory
Dome Room
Spoiler
Code: 043 (770 - shapes on wall, exactly like Sub4)
A bell is here, not that there's any sign what these new bells do, if anything, and the second green light: a leading 5.
Basement Section
Spoiler
Code: 529 (Result of equation "THIS - WX" in regards to Room 552)
This room from Submachine 4 has the last of the green lights, a 9 in the middle position.
The Green Lights
Spoiler
The green lights, like the ones before, combine to form a new code, or rather, a new legacy code.
Submachine 4 Final Room
Spoiler
Code: 596 (Green Lights)
This room contains a theory, the old exit switch (inoperable) and a new code in place of where it originally wrote its own.
New Codes:
The Lab
Spoiler
Code: 001 (596 - on wall)
This room hasn't changed from my original walkthrough, down to the bell to the left that opens the gate, although it's possible the new bells (along with the ones from 404, from the original release) factor in to whether or not the gate can open. There is still no way down the pipe here. As things stand, this a very curious end of the line.
I figured I could convert my own notes into a walkthrough for the new rooms; it happened to be the most productive use of a free period I could think of! (I'm using the room names assigned by the good people who upkeep the Submachine Wiki rather than ones of my own fabrication)
Exploration:
Spoiler
A new co-ordinate has been added to the computer list, so that should be your first port of call:
The Ouroboros Tunnel
Spoiler
051 - (000 Computer List)
The theory in this room contains quite a few co-ordinates, but they're all ones that can be accessed from other rooms. The two new codes are at the far left of the location, deduced from the symbol on the wall.
The Twins Room
Spoiler
523 - (the left hand side of the symbol in 051)
Here's a first for the Subnet; an inventory based puzzle! It's not particularly tricky, but it gives you access to a whole bunch of theories. The code in this room can be found by examining the statues; more specifically, their feet...
The Looping Sphere
Spoiler
917 - (the right hand side of the sybmol in 051)
This loop is somewhat more confusing than most of the others you'll encounter. In order to power up the screen and read the theory in this room, you'll have to work with wisdom gems, either by removing the one powering the portal and using it to boot up the monitor or (recommended) stealing another from another location in the Subnet and using it here. Either way, if you don't read the theory, you won't spot the clue to a new co-ordinate at the bottom of it...
The Broadcasting Center
Spoiler
277 - (count the strokes on the bases of the statues in 523)
This is a very impressive location (I do recommend looking out of the windows) and, although it doesn't clue to anywhere new (the theory notes two locations that are accessible through other means), you will want to grab that key...
The Clockwork Room (area 2)
Spoiler
011 - (use "smartguy-4989" at the bottom of the theory in 917; 5000-4989=011)
As much as I'd like to argue that the pins on the noteboards correspond to location codes (some of them do, honest!), the room on the right at the end of the corridor contains the only two proper clues, one old, one new...
The Defense Network (area 2)
Spoiler
128 - (add up the numbers on the panel in 011)
The only clue in here can be found on the panels surrounding the main monitor displaying this location's theory.
The Broken Clock Room
Spoiler
987 - (follow the directions on the screens in 128 - from "start right", go to the screen on the right and so on)
This is easily my new favourite room in the Subnet, but still. The clue here is "Protocol Accordant Retreat = THIS - QI"; make a note of it, since we'll find out what QI is in a minute...
Further Exploration
Spoiler
The Laboratory Key
Spoiler
With the key found in 277, you can open the door in 001 (known from Sub4 to be "The Lab"). Here you will find a device linked up to an unpowered screen; to proceed, you'll have to power up that monitor...
The Void
Spoiler
613 - (power up the monitor in 001 using a wisdom gem)
The clue here is at the very, very bottom of the ladder...
The Ziggurat (area 2)
Spoiler
157 - (found on the note at the bottom of the ladder in 613)
There is a plaque here like the ones scattered elsewhere in the Subnet, blending in against the wall.
The QI Equation
Spoiler
The clue "QI = THIS + 475" in 157 gives the value of QI, which can then be used with the hint in 987 to produce the final co-ordinate:
Murtaugh's Room
Spoiler
355 - (the plaque in 157 puts the value of QI as 632, so the clue in 987 becomes 987-632=355)
This is the end of the new batch of rooms, although were you playing this properly there is a clue here to the final room of the game. I shall not say much more so as not to spoil it...
304
875
218
757
399
100
232
580
006
185
712
550
411
404
258
672
317
553
010
947
555
806
461
992
923
777
103
241
FI = 342 (304 - Panel)
GI = 95 (859 - Panel)
KI = DI - GI (992 - Panel) [34 - 95 = -61]
NI = 842 (966 - Panel in leftmost room)
RI = 352 (777 - Panel)
TI = 322 (185 - Panel (obscured))
A1 = 8 (966)
A2 = 4 (966)
B1 = 5 (378)
B2 = 7 (378)
C1 = 9 (837)
C2 = 2 (837)
666 - Hell
815 - The "Lost" crash site.