- “This is where it all went wrong, Simon. Site Alpha. This is where we planted the seed to the cancer that's eating PATHOS-II.”
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Site Alpha is a restricted area at PATHOS-II located within the Omega Sector, between Tau and Phi. It was constructed by Carthage Industries as a covert research facility dedicated to the operation of the WAU, being the location of the Core Isolation Laboratory. In SOMA, Alpha is by far in the worst condition of all the sites, having no power and being completely flooded.
Alpha is a site dedicated strictly to the operation of the WAU, with everywhere in Alpha but the Core Isolation Laboratory being comprised of mostly computer equipment and engineering mainframes, an intentional design choice as the site is not to be inhabited. Instead, WAU and Alpha overseer and operator Dr. Johan Ross, the only person at PATHOS-II to have walked inside Alpha, is stationed at the nearby Tau.
Simon finally reaches the WAU’s core chamber, where the materialized form of Dr. Ross is expecting him, giving Simon a glimpse at what he refers to as the WAU's heart. Dr. Ross beckons Simon to kill the WAU and end its torturous threat to humanity.
At this moment, Simon can choose to fulfill Dr. Ross's plan and insert his hand in the WAU’s heart, which results in Simon having his hand amputated and being thrown to a corner of the chamber. Otherwise, Simon can decide to spare the WAU and leave the room, which causes an aggravated Dr. Ross to knock him out and bring him back to the WAU’s core chamber.
In both scenarios, Simon wakes up on the ground to Dr. Ross proceeding to attack Simon, either to force him to kill the WAU or in order to erase any remaining trace of the deceased WAU. Regardless of choice however the Leviathan attacks Dr. Ross from beneath, presumably killing him, and starts to chase Simon. Simon escapes the creature and starts the short journey to Phi.
- All featured complexes in the game are named after a letter of the Greek alphabet; Alpha is the first letter.
- Unlike the other sites, Alpha doesn't share a Greek letter. Instead, having an illustrated form of the WAU inside the Core Isolation Laboratory as its symbol.
- Due to the site's secretive nature, Alpha's depth is not stated, but is likely within the margin of 4,000 meters (13,123 feet) below the surface in the Abysmal Zone of the Atlantic Ocean.