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I just finished the game and thought I would try to make sense of what the order of events was from the logs and all that.

So about 200 years before the start of the game humanity had some sort of resource crisis. In order to deal with this Project Sisyphus was set up. This entailed sending seven research/mining stations far beyond the usual reaches of humanity's space travel in an attempt to find new types of resources. The Theseus station, on which the game is set, was 7 years travel from the nearest outpost and the crew were expected to remain and work for decades at a time.

The workers on Theseus find these odd rocks on the planet (Chori V) they are orbiting and the asteroids around it, including a much larger head-shaped one. Electrical and chemical activity indicates that these rocks have some sort of intelligence as well as a telepathic link to the other rocks. They are called 'The Watchers', and the 'Head Watcher' appears to show more activity than the rest.

The crew are able to create the Swapper device which somehow uses the Watcher's telepathy in order to move consciousness and is also able to create clones. When used between a couple of crew members both are perfectly healthy afterwards except for massive memory loss. Use of the Swapper is banned except for use between cloned subjects. (I guess that there is no 'scrambling' of memories given that clones will have mostly the same memories)

At some point the Watcher rocks taken aboard the ship notice that they are 'broken from the chain', I guess of the other Watchers on the planet. It seems like they start reaching out telepathically and end up harming and killing the crew unintentionally. The Watcher's have no real sense of the outside world, and no sense of concepts like death.

Most of the crew are eventually killed. However, back when the Swapper was created, terminally ill crew were allowed to donate their brains and be kept alive for research. Two of the crew, Chalmers and Dennett, decide the only way they will be able to survive long enough to perhaps be rescued is to swap their minds into these brains in a shielded area.

Around 100 years later, a scavenger ship crashes(?) into Theseus. The woman onboard explores the station and finds Chalmers and Dennett. Chalmers somehow persuades her to use the Swapper. When she creates a clone of herself, she panics and shoots the clone out of the station in a shuttle (hence this is your character at the start!). She then demands answers from Chalmers and Dennett. They mention that by coming in to their room she has broken the shield and so they are all doomed to die in a matter of hours due to the Watcher's. Chalmers asks the scavenger to swap with her so that she can 'put things right'. The scavenger is reluctant at first, but, not wanting to die, swaps. For some reason all three of them end up inhabiting the scavenger's body.

Chalmer wants to swap with the Head Watcher to take control and Dennett wants to crash Theseus into the planet in order to return the Watchers to the 'chain'. The scavenger, in despair, decides to 'merge' all of them with the Head Watcher. (I guess with the hope that she will retain her independent consciousness)

After this the player crashes Theseus into the planet. It is implied that the others have been joined with the Watchers, as some of the rocks display quotes from each character. At this point the rescue ship arrives (It says it was responding to an SOS). Unfortunately it is not equipped to safely remove your character (I think you are too heavily irradiated or somesuch).

So finally, you make the choice as to whether you swap with the rescue crewman or to stay on the planet and commit suicide by jumping into a deep chasm.

That's the story as far as I've worked it out. If anyone has anyone corrections or thoughts I'd love to hear them. I haven't even started talking about the more metaphysical questions the story poses such as whether a swapped consciousness would still really be 'you', but that could probably fill up another wall of text :P
Honestly I had no idea what was going on with the text when I passed by a rock for the first half of the game or who the watchers were. How does a rock watch anything? Does space tick? How does a rock know about ticking? How does a rock tell that it's spinning? They can communicate but what is there for them to talk about? Do they just think about the chain? But how does one mind tell that a thought came from another mind and wasn't its own thought, to be aware of the chain and if another mind has joined or disconnected from it.

I have a few theories. Someone carved the head. There must have been some organic lifeform on the planet at one time. Plus the head functions differently from the other rocks so that lifeform must have known about that function. This leads me to think that there was a civilization that was threatened and they found a means to store their consciousness in these rocks similar to what Chalmers and Dennet did. Then whatever disease threatened them went dormant to later kill the Theseus crew. But that doesn't explain why the rocks don't believe in space or understand movement in and out of the chain. Maybe they went crazy. Maybe they forget things over time.

Another idea is that the rocks are natural computers and could influence the lifeforms on the planet causing some civilization they interacted with to carve the head. Maybe not all rocks had contact with lifeforms and reason spread from those that did leaving anything not part of their chain as a legend. Maybe the rock communication is like a radio station. The more actively they thought the stronger the signal they put out became. Then any organic life died from prolonged exposure to extremely heavy EM fields.
The story was all over the place, but in total this game has the best graphics I have seen in a platformer. Ever. The puzzles are also very good, so this game is still a good game.
TheEddevilish: I just finished the game and thought I would try to make sense of what the order of events was from the logs and all that.
Just a note of appreciation: it was a great analysis. I'd never find enough time/desire to reread all the notes and assemble the pieces into one whole (and I doubt I would solve everything anyway). Thank you.