The Arks were small technologically advanced shelters meant to protect a small part of humanity, its brightest and greatest, from the destruction brought by 99942 Apophis. When they opened after at least a hundred years underground, they would provide humanity with the hope of beginning again after the destruction that inevitably would result from the Apophis' strike.
Only a select few of the Earth's nations had Ark projects executed with the utmost secrecy, with many people not knowing about them until it was already too late and the Arks were long buried underground. Each Ark site was provided with a high level of security, with armed soldiers lining every corridor and tanks emplaced on their perimeters, their supervisors fully expecting attacks from those who hadn't been amongst the chosen few to be selected to survive.
The Ark residents came from all walks of life. Scientists from every field were the mainstay of those chosen, so that there would be no problem in the new world that couldn't be dissected and a solution created, but also amongst these great minds were to be military men. In each Ark a soldier was placed. Destined to act as the leaders of each group of Ark Survivors, many of them had experienced the escalating brutality of the wars of the 21st century and were expected to conduct themselves in similar evenhanded manners in whatever world was left after Apophis struck.
Each Ark was created to be fully automated, with a computer A.I. controlling all of the Ark's primary functions, including the date in which the Ark resurfaced. This program, although it seemed to be not a true A.I., only emulating one, was meant to provide a basic interface between an Ark survivor and the vast amounts of scientific and practical information contained within each Ark. A female voice was apparently chosen as it would be perceived as more comforting to Ark survivors upon reanimation.
In the novel, Matthew Costello gives a descriptive rundown of the entire game, with definitions and great detailing on the Ark program and the Eden Project. Ark 437a was lowered into the ground by two maximum heavy duty military choppers. After the events of the strike on the Earth Ark 437a alerts Raine and awakens him in the midst of a damaging internal fire. Wearing a head piece with a face screen for breathing, Raine describes the Ark with sparking wiring, purplish smoke clouding the room and several heavily damaged cryogenic chambers. A large crack stops right next to his pod. The Ark in the novel is also two floors and holds different useful equipment and vital supplies that include tools, seeds, weapons, food, water, etc. Also in the novel the Ark emerges lop sided and Raine actually has a conversation with the onboard AI.
During the Prologue in the game Captain Stephen Hill can be heard speaking over a radio with Atlas Control (1138) following through the Ark procedures before Apophis hits. The Ark seals itself and it's occupants and then, once moved to a hidden location, is buried below the surface. Though even being below the surface, Apophis was so damaging to the planet that earthquakes shook up most of the Arks that lay in the ground. However, not all of the Arks were damaged because of the destruction wrought by Apophis. Some Arks were broke open before they went under by those who hadn't been chosen, their technologies ruined and the soldiers and Ark residents brutally murdered in misconceived acts of revenge.
At 9:30 AM of June 11th, 2114 (approx.) the protagonist is reanimated by the Ark 437a' computers and awakens to the Ark's A.I. and computer systems. It states that the Ark has been forced to resurface due to detection of pressure exceeding it's thresholds, as well as fires in some areas (presumably as a result of the Ark being breached), and prompts everybody inside to leave the Ark immediately. Unfortunately, the life support and cryogenic systems had sustained damage at some time during the century underground and the other Ark residents died in their pods. The only one to survive was the Omega 5 pod, which contained Nicholas Raine.
- Nicholas Raine's Ark 437a (Dam Facility)
- Antonin Kvasir's laboratory (Kvasir's Lab)
- John Marshall's Ark (Subway Town Resistance Base)
- An unnamed Ark in the Jackal Canyon
- Super Ark (Capital Prime; considered an in-game location albeit the Ark itself isn't seen)
- Unnamed Arks seen resurfacing in the Epilogue
- Elizabeth Cadence's Ark in Colorado (presumably destroyed)
- Antonin Kvasir's Ark (presumably destroyed)
- An unnamed Ark in Utah (destroyed)