Theories by user Latias1290.
Time Passage Theory (debunked)
Time Passage Theory
In Sub1, you find yourself in a basement. In Sub2, it was proven to actually just be a game, but that game was still working. Because there has to be a source of the energy for that arcade machine to run on, it proves that whatever energy source the Subnet uses is still operational. The Lighthouse in Sub2 is abandoned, and parts of it have caved in. This hints at a length of time that has passed between the player finishing the events of Sub1 and waking up in Sub2.
At the end of Sub2, you are teleported away into the single worst place you could have been teleported to from the Lighthouse. The Loop. Did you notice, that Murtaugh calls this place timeless? That means that there is absolutely zero time passed between you being teleported there, and escaping and being teleported to the Lab, at least from the perspective of an observer (clarification: This theory does not imply that there is someone watching you, but if there was, to them, everything that happened in Sub3 would have passed by instantly).
In Sub4, Murtaugh is alive, as confirmed by the fact that you can ping him, and he can communicate back. The power source is still alive, as the computer you use to communicate with him and portals are still functional. However - we are not actually sure if the man-made portals that humans use to travel around the subnet actually teleport the objects they teleport instantly, or if there are a couple of minutes of time between the subject entering the teleporter, and arriving at their destination. That's the first piece of time difference weirdness we find in the Subnet.
In Sub5, the same thing. Murtaugh is still alive, as it might very well be that Sub4 happened chronologically the day before Sub5. And the teleporters from the 1950s used to transport around the Root might as well be even worse in terms of time difference than the more modern portals in Sub4.
In Sub6, the last piece of evidence of Murtaugh being alive is given; he abandons you in the dark pit that is The Edge, which also just lost power. You are to die of dehydration in a few days, but you manage to escape and get to the Core.
This is where the first major evidence of time difference is found. In the end of Sub6, Murtaugh reveals that all the time, he just wanted to invade the Core, and you made it possible for him to do so by shutting down the defense systems. And when you get to the core, the place has already been destroyed. That is, the front of it. Murtaugh is unable to get to the inner Core, where everyone used to live, because he didn't know that hitting a gong caused a portal allowing access to the inner Core to regain its original, functional, state. When you did that, everyone already left, because Murtaugh already managed to destroy most of the outside of the Core. That didn't go without a lot of noise, alerting everyone in the Core. They all left, and when you came there, it was barren. And the reason why you seemed to get there moments after Murtaugh announced his true intents, is that by using the portal you are sent from the Outer Rim to the center of the Subnet, quite literally the biggest distance you could possibly travel with a single teleportation. And while it is not part of this theory that the amount of conductor spheres a teleporter has affects its operation, the one you used to escape from the Edge has two spheres, whereas every other one has three. This may be another factor, but this theory has no implications on that.
At the end of Sub7, you enter a green karma portal, a color which has not been seen before. You enter, and you are sent into the nothingness. The portal has no destination. This is where the vast majority of time in the timeline of the series has passed. If you go through a regular karma portal, it takes 0.1 seconds to go to the other side. (In Submachine Universe, this can be up to 5 seconds) While not long, it does prove that the karma portals do not take zero time to teleport an object from one location to another. And then, most karma portals are situated from their counterparts within, something like, no more than 200 meters. What if you made a karma portal that teleported an object hundreds or thousands of kilometers away, or more? That would take a long time. By the time you arrived at the Dock, Murtaugh and Elizabeth died long ago. You even found their corpses in the next game.
In a nutshell, you are late. Hundreds of years late. Sub10's Secret Area (if it has one) might contain lengthy pieces of text detailing what has happened.