Simon gradually realizes the black organic growth that has consumed the facility is PATHOS-II's artificial intelligence, the WAU. Together, Simon and Catherine struggle through the ruined facilities of PATHOS-II, with underwater hikes between each site, and numerous hostile creatures attempting to stop them from proceeding. The ARK currently resides in site Tau, a PATHOS-II facility at the bottom of a deep chasm called the Abyss. But the project was permanently suspended when, despite her best efforts, several crew members killed themselves after being scanned to ensure the only true copy of themselves left was on the ARK itself.Д¬atherine then attempted to take the ARK down to the Space Gun, but there were complications and the launch never occurred. Catherine's 'original' self scanned many PATHOS-II crew members into the ARK. Launched into orbit by PATHOS-II's Omega Space Gun and powered by solar panels, it would safeguard humanity's last remnants for thousands of years. She then enlists his help in finishing her life's work: The launching of the ARK, a simulated reality for a collection of human brain scans. But the facility was heavily damaged and the crew realized they only had months to live themselves.Д¬atherine soon asks Simon to transfer her into his Omnitool. PATHOS-II was the only place where humans survived the comet's impact. It is also revealed that the surface of the Earth was recently struck by a comet, devastating the planet and killing all life on the surface. Simon's copy had somehow become mysteriously activated on PATHOS-II.

Simon's brain scan, being one of the first, became widely distributed among other medical professionals and students for learning and experimentation.

This allowed Munshi to narrow down a treatment plan for his neurological condition. When Simon got his brain scanned by Munshi, a copy of his consciousness was saved to the computer. She then reveals that Simon himself is also not human, but a Cortex Chip implanted in a dead woman's body, Imogen Reed, wearing a Haimatsu Ductile Suit, and that the 'original' Simon has been dead for a hundred years. Simon then discovers that Catherine is not human, but a scan of a human consciousness placed into a robot's body. There are no signs of any normal, living humans, though Simon does encounter a few robots who believe that they are human, as well as other robots that act as some of the protagonists of the game.Д«efore Simon reaches Catherine upon arriving at site Lambda, she is heavily injured by a humanoid creature. The walls are slowly being covered by a black, seemingly organic substance, that sprawls across the entirety of PATHOS-II, as parts of the facility are blocked off and destroyed by it. It quickly becomes apparent that PATHOS-II is an underwater facility in serious disarray. Simon manages to find an Omnitool and eventually comes into radio contact a woman named Catherine Chun, who tells him to come to site Lambda and meet with her. The combination for the locked back-door in a journal, he meets with David Munshi, who reassures Simon that the scan will feel about as uncomfortable as 'having your picture taken.'ДЄs Simon's brain is scanned, there is a bright flash, and Simon suddenly wakes up in PATHOS-II, at a site called Upsilon, without any idea of how he was transported there or what is going on. He discovers an office closed for remodeling, with no one at the front desk. After locating and taking the fluid, he departs for PACE Laboratories. He wakes up in his apartment and receives a phone call from David Munshi, who reminds him that he has to drink Tracer Fluid before the scan. The game begins after a brief cut-scene in which Simon has a nightmare of the aforementioned crash. Because of the lingering effects of the crash, Simon agrees to an experimental treatment involving a brain scan. Simon survived the incident but was left with permanent brain damage.

The main protagonist of SOMA is Simon Jarrett, who, prior to the events of the game, was in a fatal car crash that killed his friend and passenger Ashley Hall. The only way out is to do something unimaginable. The world around them is turning into a nightmare. Machines are taking on human traits and alien constructions have started to interfere with routine.

As isolation bears down on the staff of the remote research facility, strange things are happening.

Soma crashes on launch