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- "This is where it all went wrong, Simon – Site Alpha. This is where we planted the seeds of the cancer that is eating PATHOS-II."
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By the events of the game Alpha is by far in the worst condition of all the sites. It is completely flooded and has no power, and is completely being taken over by WAU.
Simon finally reaches the WAU’s core chamber, where the materialized form of Johan Ross is expecting him, giving Simon a glimpse at what he refers to as the WAU's heart. Ross beckons Simon to kill the WAU and end its torturous threat to humanity.
At this moment, Simon can choose to fulfill 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 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 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 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 attached to a triangle 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.