It currently impossible to find a concise summary of events for the main series of Submachine games made by Mateusz Skutnik. For my own sanity, and in case anyone else ever needs it, I pieced together the story by replaying the entire thing and making notes. If anyone ever benefits from this, my weekend of work will have been worth it.
Submachine 1 - The Basement: The player enters the basement, solves a few puzzles, collects four triangular pieces that form a diamond and open a door to the outside. We learn about Murtaugh (Mur) through a note, and that he lost his arm on a camping trip to Kent and, in its place, found seven new arms instead.
Submachine 2 - The Lighthouse: The outside is a set, and the player moves on to the lighthouse. There, we're introduced to Elizabeth (Liz) as well as Einstein, the cat. We discover the lighthouse where Mur worked as a wickie, the digouts in the basement, and the portal prototype in the lantern. He is obsessed with entering the submachine network he discovered in the digouts, that his predecessor left there, and to explore it. We power on the portal.
Submachine 3 - The Loop: The lighthouse portal should lead us to the lab, the base of exploration on the outside of the submachine network or subnet, but the subnet's defence system captures the attempted teleport and places the player in the Loop, an infinite non-space that generates endless puzzles for people to get trapped in and die of dehydration. Before the player does, they find a note from Murtaugh, telling them to find a green leaf and bring it to a statue hidden deep in the loop. The player does so, and are disconnected from the loop.
Submachine 4 - The Lab: The loop releases the teleport and the player manages to land on the roof of the lab. They make their way inside, where they find a computer that's connected to Murtaugh's computer, but the keyboard is broken. They get an assignment from Mur - to find the exit of the small patch of subnet and to solve its puzzles on the way there - and manages to "pass all the tests".
Submachine 5 - The Root: The player awakens in the second Lab, deeper inside the subnet. There, Mur has left instructions for them to find three shards of crystalline energy, known as Wisdom Gems, and use them to power a craft that leads them deeper into the subnet. To do this, the player investigates the first submachine - the root - and retrieves the three shards. It's also revealed that the root was behind a walled off door in the lighthouse, but the lighthouse is inaccessible. They power the mover and float into the void.
Submachine 6 - The Edge: The subnet's defence system, powered by the AI SHIVA, intercepts the mover and - upon being unable to identify the player as an authorised user - dumps them on the edge of the complex, where they're left to die. They explore the limited area, and make their way into maintenance tunnels, where earlier groups of Mur's explorers had set up camp. They're nowhere to be found, and notes indicate that they jumped off the edge to avoid death by starvation. The player enters the defence system facilities and acquires a connection pod that lets them interface with the AI's VR computers. There, they disable the secondary and primary defence systems - large sentry guns perched on the Edge, a massive wall that seems to stretch all the way around the inner submachine - and shut down the mainframe's verification algorithms. Murtaugh is impressed, says that they can finally invade the core, and tells the player that their adventure ends there. He disconnects the computer. The player scrambles on top of the edge wall, where a portal is placed. They connect the pod and are teleported somewhere unknown.
Submachine 7 - The Core: The player arrives at Sanctuary - a place in the inner submachine, but otherwise unspecified. Sanctuary seems like a Hindu temple at first, but military supplies as well as abandoned machine guns litter the place. The player collects three stones to power an ancient gateway and passes through, leading them to the Winter Palace. The Winter Palace is a vast and expansive garden built by The King's urbanist, the same man that built the lighthouse and - it's implied - the root. The palace is closed down, but a portal in the wall lets the player go through the wall. On the other side, Liz left a note telling the player not to use these "karma portals" again, as they damage the very fabric of reality. Murtaugh has been placing them using his karma arm, the one that replaced his actual left arm. The player makes their way through the core and eventually calls Liz' ship down to the docks, which we enter. The inside is littered with bullet holes, and a note from Elizabeth telling the player that she left in a hurry to escape Murtaugh, who has been besieging the palace in an effort to exploit and weaponise the submachine. She fears that with one more Karma portal placed, reality may collapse entirely. We see what's left - a large green karma portal out into the void - and follow her.
Submachine 8 - The Plan: The Karma portal also contains echoes of Murtaugh's memories. He explains to Liz that if he places a portal while inside another portal, he "changes direction". When Liz asks what direction, he replies with "everything". The player arrives at a new location - a barely holding together plank construction in the middle of the void, some sort of listening or receiving outpost. They climb down and find the Navigator - a device built by Murtaugh that lets them change their attunement to the Layers of Reality. They learn that the location they're in is called Sector Nine, a smaller submachine, and it's a unique place in the subnet as it occupies all seven layers at once - but is vastly different in each layer. This concept, an architectural idea that spans all seven layers in an interlocking way, is called The Plan. The first layer is the listening post, the second layer is a palace, the third layer is a garden of sorts, and so on. The player activates all the beamers - structures that enable the Navigator to access different layers - and leaves through a gate of light.
Submachine 9 - The Temple: We arrive at The Temple, a large structure near the centre of the subnet. The player solves the puzzles required to reach the bottom of the Temple - a place called the Knot - where they find the tombs of Murtaugh and Elizabeth. The player learns about Murtaugh's powers, and how creating a portal works - Murtaugh was in all layers at once, and to be in only one meant to "lose focus". To his followers this appeared as though he was a ghostly spectre, and they believed he had abandoned them, especially the teams in the Plan. It's also revealed that SHIVA granted Murtaugh his powers, somehow. The player finds the eighth button of the Navigator, and enters the layer of light, where time stands still and friction of the still atoms creates permanent trails of light. They touch the white karma portal created by Murtaugh, and are brought back to the Winter Palace.
Submachine 10 - The Exit: The player arrives at the Northern Docks of the Winter Palace and enters the captain's ship, which is heavily implied to be that of Murtaugh or one of his explorers. Inside, there is a Karma portal to a corrupted, much older version of the lighthouse, from which the player accesses Murtaugh's laboratory in the subnet. We learn that he was working on a way to reverse the damage caused by karmic energy, to stabilise the rifts he had caused, and that time travel was an inevitability in the subnet - a loop can not only repeat space endlessly, but time, and could thus be used as a way to time travel if one timed entering and exiting correctly. They also find the AI core for SHIVA. SHIVA was built as a mind for the subnet, which it treats as its body - not much is known about the supercomputer, only that it became sentient shortly after being asked the question "Why are we?", which it knows the answer to, but hasn't revealed to anyone. It also had taken over the defence systems as a way to protect the subnet against the "human infestation", and to isolate the very purpose-built core against the outer rim, which was growing uncontrollably by way of Murtaugh's discovery of the subnet in the first place. He wanted to map it, so the subnet grew, making it essentially unmappable and ever changing. The player shuts down SHIVA and proceeds to rebuild the destroyed structures of the subnet by finishing the Karma Stabiliser that Murtaugh never completed. Once complete, the player ascends the lighthouse and leaves the submachine - to find Murtaugh and Elizabeth on camels, in a desert, the lighthouse lantern barely poking out of the sand, with two suns in the sky.