The Nightfall Program was a research project lead by Captain David Archer. Archer founded the program in 2016, a year after encountering a Cryptid colony during the Tel Aviv War. The program consisted of at least 127 scientists and employees based out of Point Barrow, Alaska, the site of the project's headquarters. While its benefactors believed it was investing in biochemical weaponry, Nightfall's true intentions were to investigate a means of severing the ties between the Cryptids and their masters, gaining control of the creatures themselves. However, they were dissolved after the events of Awakening as David Archer dies during the events of Awakening following the destruction of the Ball's Pyramid Ark.
After locating a colony of Cryptids in Swat Valley, Pakistan during an SAS operation, David Archer became infatuated with the alien ecosystem living beneath the earth, more so the unseen forces manipulating the creatures behind the scenes. Hiring dozens of world-renowned scientists in various fields of profession, Archer founded the Nightfall Program, establishing a remote facility in Point Barrow, Alaska as its headquarters. In order to obtain funding, Archer posed the project as a biochemical weapon business, it's benefactors assuming the Cryptids were end products of their work. However, the true purpose of Nightfall was much more sinister; to find a way to seize control over the Cryptids for Archer's own use.
During an archeological dig, Nightfall uncovered numerous structures surrounding a Cryptid meteor covered in complex hieroglyphics, showing signs of Mayan and Akkadian influence. Proving too difficult to translate, Archer realized he would be forced to make new additions to his team to continue his plight, and found the answer to his dilemma following an interview with Samantha Cross of Harvard University. Possessing a rare gift to translate languages with ease, Cross was employed by Archer and flown out to the head Nightfall facility to begin her work.
Following the ODIN Strike that decimated the American North and Southwest, a colony of Cryptids beneath the Colorado Rockies was exposed, releasing them back to the surface of the Earth. The rumors of an outbreak in Caldera Peak, Colorado intrigued Archer, prompting him to lead an investigation of the site with the intent of evaluating the military potential of any new species they found. He returned with numerous Cryptid samples and a large obelisk carved of obsidian rock and inscribed with Cryptid hieroglyphics, known as an Obelisk. As Cross began tirelessly decoding the Obelisk, Archer expressed interest in finding more of the items globally, believing one to be located in the South Pacific that inspired the lost continent of Mu. Requiring a ship and crew, he began covertly negotiating with a Chinese client known only as Contact 28, offering Nightfall's impressive weaponry and research to the country in exchange for his requests. Meanwhile, Cross, now fearful of Nightfall's true intentions, breached the location of their head facility to the U.S. government, as well as sabotaging the hatchery under the influence of the Cryptid masters.
With over 100 employees killed in the outbreak, Nightfall was deemed terminated by the U.S. after the Rapid Reaction Force pacified the overrun facility. However, the few who survived the outbreak, including Archer and a captured Dr. Cross, attempted to recover from the fallout and sailed for an Ark aboard Stormbreaker, Archer's vessel supplied by Contact 28. Onboard, the survivors focused their attentions on experimenting with anti-Cryptid technology to protect themselves from another attack, as well as the defecting Samantha Cross, who was surgically bonded to the Beacon Amplifier to aid them in their travels. However, problems arose when the crew began experiencing vivid nightmares from the increasingly-hostile presence of Cross, rumors threatening a mutiny and even some going against Archer's commands. After many abandoned ship to keep their lives and sanity, Cross summoned the Arks' aquatic guardian to keep Nightfall from reaching their goal, igniting a third outbreak in the process. By the time the military arrived and defeated the Cryptid enemy, Nightfall had completely dissolved, Archer himself defecting as a double-agent to the United States.
Despite Archer defecting to Godfather, Archer's luck started to run out. First, Archer and two American soldiers were cornered by dozens of Cryptids beneath the surface of Ball's Pyramid, which eventually causes a Gargoyle to attack one of the American soldiers, who was pulling the pin on a grenade at the time. Archer uses the other soldier to survive the explosion, but is blow back, scrapping his arm against a Cryptid plant, infecting his entire right arm. Samantha Cross, who was assumed killed following the the destruction of the Stormbreaker, appears and tells him that the poison is deadly, which Archer replies that all of this is a dream. Cross then proceeds to serve Archer's right arm, saving him with the intent of cutting a deal with him.
Cross' deal consisted of her leading Archer and his remaining troops to the Ark in exchange of her safe return to the USA, which Archer reluctantly agrees to, although he has second thoughts. After obtaining the Cortex from an Ancestor from within the Ark, Archer then betrays Cross, but Cross uses her telekinesis to make Archer shoot his remaining troops dead before forcing him to shoot his own left leg, crippling and disabling him. Cross then leaves Archer for dead as CIF Team One eventually reaches the Ark sometime later to finish the job. After CIF Team One obtains the Cortex, they leave Archer behind, where he then dies from the meltdown. With Archer dead, the Nightfall Program was completely dissolved, with Cross being the only surviving member left.
- The Venom-X, a powerful projectile-based weapon that harnesses the toxic biolum of Scorpions to fire the same poisonous gas. While aboard Stormbreaker, the surviving Nightfall scientists varied the type of biolum used to produce the weapon's ammo, leading to several different variations of the gun:
- The Venom-FX, which produces fire damage.
- The Venom SX, which spawns friendly Seeder spores.
- The Venom LX, which produces electric damage.
- The Breeder, a large arachnid-like Cryptid hatched in the head Nightfall facility in an egg sack the size of a trailer. The creature was designed to produce more Cryptid specimens to be used in Nightfall's research, however it was disposed of during the Rapid Reaction Force's raid on the facility.
- The Hypno Trap, an anti-Cryptid device designed by Archer aboard Stormbreaker. The weapon acted as a pressure plate that utilized and amplified the ability of the Hypno Knife, allowing even a Rhino to be hypnotized by it.
- The Tesla Trap, an anti-Cryptid device designed by Archer aboard Stormbreaker. It acted much like a Tesla coil, primarily used to electrocute any nearby Cryptids. When placed near another Tesla Trap, the device would connect and create an electric barrier capable of electrocuting anything that passed through it.
- The Beacon Amplifier, a device designed by the world-renowned neuroprosthetic scientist Dr. Kassar aboard Stormbreaker. Fused with Cryptid plant life, Cross' brain was surgically bonded to the device as a means to aide in the voyage to the second Ark. After CIF Team One pacified the outbreak aboard the vessel, Cross disappeared along with the Beacon Amplifier.
- The Cortex Holding System, a device that holds one of the Ancestor's soft tissue, which is key to stopping the Ancestors from world domination and part of Archer's plans for his Medusa weapon. The Rapid Reaction Force obtains the Cortex from Archer within the heart of the Ark and escapes Ball's Pyramid with it.
- The NX-1 Disruptor, a powerful weapon designed by Archer. When shot, it will shoot a lightning-like shot, which can kill weak Cryptids in one shot. When fully charged when holding down the trigger, it'll create a ball of energy which can destroy an Ancestor's shield in one shot. It also can regenerate ammo, either while in use or stored away.