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In PATHOS-II, Imogen Reed found a machinery modified by WAU, who was acting on its own, called the Vivarium, that could produce a virtual simulated reality. At the time, Catherine, who was developing a AR-capsule to run primitive neurograph models, updated her project based on the Vivarium originating the ARK.
The ARK consists of a virtual simulation of the world including modular space, mixed deciduous forest, and an urban park, in which the brain scans made of PATHOS-II employees could be uploaded to and experience a simulated reality. It was designed to be launched into space with the Omega Space Gun and, in theory, last for thousands of years powered by solar batteries.
After the Impact Event destroyed all life on the Earth's surface, the PATHOS-II survivors made the ARK top priority in hopes of saving at least a small part of the human race.
In the end of Transmission #8 we see images from inside the ARK on the walls of Upsilon where, on a sunny day, the uploaded brain scans of Adam Golaski and Imogen Reed embrace.
Sometime between November 1 and December 25, 2103, a party formed by Catherine, Sarah Lindwall, Nicolai Ivashkin, Ian Pedersen and Jasper Hill left Theta in order to complete the ARK project. On December 27, the ARK team arrives at Site Phi in order to launch the ARK into space with the Omega Space Gun but the group opts to postpone the ARK's launching and returns to Tau to figure out their next plan of action.
In Lambda, Catherine informs Simon of the ARK project and asks him to determine the vessel's whereabouts. Simon finds a terminal containing information about the ARK vessel, including its approximate location via a built-in tracer. Using the tracer, he finds that the ARK is currently situated in Tau. From this moment on, simon travels through the many stations of pathos-ii with the completion of the ark project as his main goal.
While crossing Theta's main laboratory section, Simon finds an ARK prototype from which Catherine collects data.
In Tau, Simon finds the ARK under the guard of the last surviving human being, Sarah Lindwall. After conversing with her, she allows Simon to take the ARK to launch. Simon transports the ARK in a cargo hatch leading to a separate Dive Room, where he is able to hook it onto a cargo transport system leading to Phi.
In Phi, searching through the lower level of the station, Simon finds the ARK intact and still hooked to the cargo arm. He carries it to the assembly space and loads it into the Space Gun's missile shell. Both Simon's and Catherine's consciousnesses are copied onto the ARK and it is launched.
The Simon copied to the ARK wakes up in an idyllic landscape, completely unaware of his other version left behind on PATHOS-2. He is soon reunited with Catherine in front of a futuristic island city. Meanwhile, it is shown that the ARK successfully makes it into space as it leaves behind a devastated Earth, ending the game.