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.
CIF Team Four of the Rapid Reaction Force is dispatched to the quarantined site at Caldera to investigate, and are killed by the invading Cryptids within the first hour of deployment.
A four-man squad from Task Force Spectre are sent to exterminate the infestation of Cryptids via nuclear detonation authorized by the President and use a mounted Laser Drill to destroy Cryptid hives.
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.
CIF Team One is sent to Point Barrow under the direction of General "Godfather" Castle to rescue Samantha Cross, who has been hiding in the research lab.
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.
Cross alerts the Ark's guardian as Stormbreaker approaches the colony, and the Kraken is awoken.
Godfather launches Operation: Mayday; CIF Team One is dispatched to Stormbreaker to pacify the third Cryptid outbreak and recover Archer as a double-agent.
The Kraken is killed by the military, Archer is evacuated, and Samantha Cross is declared KIA after disappearing.
Cross is telepathically summoned to the Ark beneath Ball's Pyramid, where she foresees the end of the world.
Godfather torpedoes the contaminated Stormbreaker to ensure the outbreak is contained.
Archer is sent with a squad of soldiers into the Cryptid colony beneath Ball's Pyramid to obtain the Cortex.
The Ark is overrided with geothermal heat and CIF Team One escapes with Cross and the Cortex.
The remaining Arks are awakened and the planet is overrun with Cryptids, forcing Godfather to launch nuclear strikes on key infestation points in Operation: Scorched Earth.
The Arclight osprey crashes in the heart of the outbreak, leaving CIF Team One stranded and Samantha disappeared with the Cortex.
Cross is willingly placed in a replica Beacon Amplifier to allow her powers to be amplified, intending to make humanity's difference between survival and extinction.
Pockets of resistance in Europe and Asia continue to fight Cryptids. The Cryptids are eventually defeated, and humanity rebuilds, expanding into the stars afterwards.
