Earth, originally a dark planet covered in volcanic ash, is hit by a comet that incinerates the atmosphere and everything that lived on the surface. The Cryptids survived by living within the earth's chambers, where they evolved and adapted to survive underground in harsh climates.
The Ancestors forge the Arks, geothermal reactors designed to reawaken and rise above the Earth, and the Obelisks that protect them.
An aquatic guardian is bred by the Ancestors to deal with any threat to the Arks.
The ODIN Space Station is attacked and hijacked by astronauts of the Federation. Tungsten Rods are then launched, destroying the majority of the south and southwestern United States. Two surviving American crew members, Mosely and Baker, fight back and scuttle the space station before the remaining rods are launched on the remaining U.S. cities, but sacrifice themselves in the process.
A stray Tungsten Rod impacts a Cryptid colony beneath the Colorado Rockies near the town of Caldera Peak, Colorado.
The Ancestors command the Cryptids to attack, and Caldera Peak is eradicated of all life.
Archer and the Nightfall Program locate the Cryptids in Colorado and collect as many specimens as possible, as well as an Obelisk.
Archer hatches a new Cryptid species, the Breeder, of monstrous size. Cross begins to fear the Nightfall Program's work, and compromises the location of Nightfall's facility to the U.S. military.
Archer barters with Contact 28, exchanging Nightfall's research for a ship and crew.
Cross suffers from the mimetic virus infused within the Obelisk, and begins acting under the control of the Ancestors. She breaches Nightfall's hatchery, ensuing an outbreak that slaughters 127 of the Program's employees.
Archer reconciles with Contact 28, who agrees to supply him with an extraction.
Cross prepares to kill herself after finishing the Obelisk's translations, but is captured and taken into the Alaskan Frontier by Archer, who escapes with her aboard Stormbreaker, a decommissioned destroyer given to Archer by Contact 28.