The Green Light Theory [read only after completing Submachine: Legacy in its entirety!]
The dust is settling around Submachine: Legacy, but one of the questions that is still up in the air is "what's the deal with all of those green lights in all the games?". I'll try to answer that in this theory.
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[spoilers ahead, last chance to look away]
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Some theories have been floated already in the community (now almost entirely on Discord) and they seem to coalesce around three main ideas: 1) there's a secret hidden puzzle that all of them are part of, 2) they denote the location of secrets, or 3) they signify the fact that SHIVA/the Subnet has been busy intertwining itself with the rest of the games and making its presence known.
I noticed them just like anyone else during my playthrough, and did initially wonder if they were tied to the secrets system, but if you take the time to look at where they actually are placed in the games, that's clearly not true, especially since about a third of them appear in Shattered Quadrant, which has no secrets. After doing a complete playthrough of Legacy, the conclusion that I reached fell more in line with the third idea, specifically that perhaps this is SHIVA's way of restoring all of the previous games' areas to full accessibility in the seven main layers, which is a delightful and intriguing development that calls into question previous assumptions made by the idea of the Knot/Temple being a unique place, and more importantly, whether Submachine: Legacy exists in its own spot in time rather than being the one version of the games that is meant to exist.
However, I just wasn't content with this being the idea, as it doesn't account for the specific placement and dispersal of said lights. As someone else initially pointed out, no lights are present in Sub9, and three of them alone appear in one single location in Shattered Quadrant. I also personally couldn't stop thinking of the one specific instance in Sub2's sewers, where one appears almost exactly where a secret used to be. It made me wonder if other lights appeared in spots where things have moved or shifted around. So, the natural next step is to document where all of the lights appear.
Below is a list of all occurrences of said lights, abbreviated by game for easy reference. Also note the usage of terms consistent with names/coordinates used to describe locations in the games - particularly Submachine Universe - before Legacy was released.
1-BE - Sub1, appears in basement exit (and also again in sub10 in the same spot)
1-BTN - Sub1, appears in BTN location
2-LT - Sub2, appears in lighthouse tower just below second floor
2-SW - Sub2, appears in far left of sewers
3-LS - Sub3, appears in fka. looping sphere location
4-AS - Sub4, appears in ancient section
4-LD - Sub4, appears in lighthouse digouts
4-LO - Sub4, appears in looping traps
4-KOL - Sub4, appears in fka. resin temple location
5-CR - Sub5, appears in (0,1)
6-CL - Sub6, appears in cliffs above rightmost pipe
6-DS - Sub6, appears in the DS, in the lower part of area 4
7-WP - Sub7, appears in the entrance to the atrium
8-L6 - Sub8, appears in Layer 6/the armory
10-BS - Sub10, appears in OOO > sub1 basement
10-MS - Sub10, appears in "metal section" on other side of the 4-tile door
10-LO - Sub10, appears in IOO > sub3 loop
10-KR - Sub10, appears in IIO in the room with the big tank of karma energy
10-NG - Sub10, appears in OOO in the Northern Garden Docks by the docking schedule
10-RS - Sub10, appears in IOO in storage unit 33/3
10-SH - Sub10, appears in OII on landing SHIVA bubble
10-ST - Sub10, appears in IOI by the data disc storage
SQ-888 - Shattered Quadrant, appears in cube loop
SQ-AEL - Shattered Quadrant, appears in Murtaugh's observatory unit > cat > ael
SQ-CAT1 - Shattered Quadrant, appears in Murtaugh's observatory unit > cat (landing screen)
SQ-CAT2 - Shattered Quadrant, appears in Murtaugh's observatory unit > cat (left of landing)
SQ-CAT3 - Shattered Quadrant, appears in Murtaugh's observatory unit > cat (right of landing)
SQ-DEF - Shattered Quadrant, appears in pre-shift transit station > def (blue defsys room)
SQ-GLO - Shattered Quadrant, appears in brass hatch > glo
SQ-728 - Shattered Quadrant, appears in right side of the rift > lucky room
SQ-FAR - Shattered Quadrant, appears in pre-shift transit station > far (purple room)
SQ-006 - Shattered Quadrant, appears in iron triumph loop
SQ-316 - Shattered Quadrant, appears in laser junction infiltration station
SQ-WIQ - Shattered Quadrant, appears in Ouroboros ruins > wiq
When looking at the locations of all the lights, it becomes immediately clear that a lot of them exist in places where specific things have been altered from previous versions of the Submachine games for specific purposes, either in place of things that have been removed, or in close proximity to things that have been changed. I believe the green lights are best read as a sort of signature or footprint that Mateusz Skutnik left, signposting the types of changes he made to a wide range of elements in the games, in order for the Legacy to happen.
Six lights appear in places where theories previously seen in SubVerse locations have now been removed (SQ-CAT2, SQ-CAT3, SQ-GLO, SQ-006, 1-BTN, and 3-LS). This speaks to Mateusz Skutnik's commitment to remove all writings of people besides him to retain full intellectual property of the content in his games. Likewise, SQ-316 appears in a spot where the pictures in the viewers have been switched from what were presumably Mateusz's own personal pictures to pictures that more appropriately fit the game universe.
Three lights appear in spots where secrets have been removed, changed positions, or added (2-SW, 4-LO, and 10-RS), speaking to Mateusz's restructuring of the secrets system. 4-KOL is in a spot where a clue from the historical SubVerse clue system used to be, signaling how that system is now obsolete in Shattered Quadrant.
8-L6 (sadly) removes a note and mysterious graphic that was never fully explained in previous iterations of the game. While it will be missed, it shows that Mateusz was focused on removing some things that he didn't intend to ever fully explain.
4-AS brings the new extension of the Ancient Section from SubVerse into Sub4, and also points to the new secrets system in the process.
4-LD is shown on the same screen where more graphical details have been added to the bricks and stones, which is either an example of how Mateusz has gone and retouched the games, or how this specific location has aged since we last saw it (or potentially both). Similarly, 6-DS appears in a spot where the security barrier has been re-drawn with better graphics.
SQ-DEF is shown above the grate where there now exists a vertical collection of lines in addition to the horizontal collection, which helps further clarify that this puzzle needs to be solved in two parts.
SQ-AEL is a bit harder to tease out, but the notable change on this light's screen is the addition of shards, which could point to the shard engine that was implemented across all games, where all shards now can be pushed around and will eventually return to their original positions. This could be easily considered a weak link to the hypothesis, if it were not for Mateusz previously sharing demos and public adoration of this shard engine system in years past.
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Uniquely, 6-CL exists on a screen where no changes have been made, but will be made in a later chapter when the cliffs are revisited. This suggests a more cognizant effort to tie all the chapters together and also hints at the green lights being indicative of a system that knows how future chapters will play out.
A few lights appear in places that make me think they're there to represent changes that take place in the whole area, not just one screen.
The one that appears in Sub1/Sub10's basement exit, 1-BE, is significant because the transition between Sub1 and Sub2 has been completely rewritten, which is a larger change in the narrative that allows that area to be visited as early as Sub1.
SQ-888 probably exists because the loop structure of that area has been changed to get rid of the extra rooms and "trim the fat", so to speak. It now appears on the only screen that doesn't have a portal or a note (totaling 3 rooms in the loop now, as opposed to 9 in SubVerse)
SQ-WIQ exists to point out how much of the extensive WIQ location has been condensed from SubVerse.
SQ-728 similarly exists in the lucky room, which has had all previous secrets from Sub4 and Sub5 removed in order to better work with the new secret system, and has also gone a significant physical restructuring location-wide. Similarly, 10-LO exists in "Level X", which has undergone significant restructuring to the puzzle within.
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At this point, the remaining lights are hypothesized to not related to changes on the same screen, but instead are related to other changes made in the same location. For most of the occurrences where the light is one screen away from the change, I think this was done so that players wouldn't get the wrong idea that the lights somehow corresponded to the relevant objects in a way that suggested the lights needed to directly interact with them.
I believe 2-LT points to the nearby new picture of Einstein and the clarification it gives to the E=mc^2 puzzle.
SQ-FAR probably points to the nearby redesign of the lever in this location.
5-CR probably points to the nearby inclusion of a layer marker in this location.
7-WP probably points to the nearby redesign of the stone blocade puzzle in this location to clarify how the puzzle works.
10-BS probably points to the nearby picture frame that is one example of how picture frames all across the games now have hand-drawn pictures of unknown rooms in the subnet.
10-NG appears in the screen next to where the backpack used to be, showing that the new inventory has rendered the backpack in Sub10 (and the concept of having too many items) obsolete.
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Unfortunately, as one goes down this list, the justifications get less confident and apparent. There are still five lights I haven't discussed (10-MS, 10-KR, 10-SH, 10-ST, and SQ-CAT1) and that's because I don't really know why they are placed in the spots they are. There are changes in some of the locations they're found in, but not ones that appear important enough to point out. One could maybe say that 10-SH is placed in its spot because it's literally at the SHIVA access point, or that SQ-CAT1 is there because this is a location that was originally much smaller when it was first added to SubVerse, but beyond that, I have no explanations. The more solid reasons given for the lights above could also lead some to question why there aren't even more lights found everywhere for puzzles, graphics, and locations that were significantly changed (think: grate puzzle in Sub4?). Perhaps that can be chalked up to Mateusz being sparse enough so that the green light motif wouldn't be visually exhausting and boring to look at after a while, but I'm not one to say that with certainty.
Either way, the theory is a fun one to consider. It's a fun way of acknowledging the way that Mat/SHIVA has reached into all the games to tie them together and tweak them for the better, and more importantly, it spurs implications of how Submachine: Legacy should not be viewed as the one true way to experience Submachine, with all the previous versions fading into history. Rather, it's simply the latest iteration of the Subnet, which seemingly exists along yet another dimension of time that properly exists in our world as well. New players to the series might think that the Legacy is what Submachine was meant to be all along, but along with new notes in Shattered Quadrant, the green lights might hint at a hidden history that's worth exploring.
Addendum 2023-11-09: I found a third light in Sub6. Designating it as 6-MF, it's found in the mainframe, on the screen where you can see the underside of a turret. The singular change on this screen is the redesign of the indicator lights, which now glow blue-green (or the set UI color) when the turret is enabled and red when it's disabled.
Addendum 2023-11-18: Edited the section referring to 2-SW, 4-LO, and 10-RS to clarify that 4-LO was not removed from the screen, but was just repositioned.