The Callisto Protocol tells an enigmatic story about a pilot who finds himself trapped in Black Iron Prison just as a deadly outbreak occurs, which turns the inmates into zombie-like monsters. It is a tale of survival in the face of absolute horror that eventually takes a mysterious turn in the game’s final hours. This twist blows the story world wide open and reveals the dark secrets behind Black Iron Prison’s leaders and the outbreak.
[Warning: This article contains spoilers for The Callisto Protocol.]
Early in development, The Callisto Protocol was removed from PUBG’s universe, so not much is revealed about the backstory and larger universe in The Callisto Protocol’s narrative. However, the primary context for The Callisto Protocol’s story is that it takes place in the year 2320, and humanity has colonized the solar system. Many significant settlements are located on the moons of Jupiter, like Europa, and are under the control of an organization called the United Jupiter Company. The UJC operates a prison colony on Callisto called Black Iron Prison, where the protagonist finds himself inexplicably incarcerated at the beginning of the game.
Jacob Lee Crash Lands At Black Iron Prison & Is Captured
The Callisto Protocol begins with two cargo haulers, the protagonist Jacob Lee and his partner Max, watching a news broadcast about an attack on the Europa colony, which is purportedly carried out by a known terrorist organization called The Outer Way. The organization is led by Callisto Protocol's Dani Nakamura, played by Karen Fukuhara, who is shown in footage of the attack’s aftermath. Max is distressed by the report, but Jacob shrugs it off, saying that the job at hand is more important, which is delivering a cargo shipment to Callisto.
of The Outer Way then board their ship, Dani Nakamura being one of them. Jacob is almost captured by the group but manages to lock them in the cargo hold, to which Dani responds by demanding the ship, forcing it to crash land on Callisto. Max dies in the crash, and Jacob and Dani are the only survivors. Captain Ferris of Black Iron Prison locates the ship and imprisons the two, despite Jacob’s protests that he is innocent.
Once at Black Iron, The Callisto Protocol previews the gore to come when Jacob has a neural device called a CORE implanted in his neck. The CORE is meant to monitor the health of inmates but can cause adverse reactions, such as hallucinations, and Jacob faints upon receiving the device. He later wakes up in a cell to find that the entire prison is in shambles. Zombie-like creatures that used to be prisoners are attacking people, and the guards have no control. Jacob meets another inmate, Elias, a few cells down who isn’t infected and knows a way out. Elias has been in Black Iron for a long time and needs Jacob’s help to escape.
Jacob and Elias move through various levels of the prison to make their escape. They cross paths with Dani, but she leaves them to escape alone since she doesn’t trust Jacob. Jacob and Elias move further through the horrors of The Callisto Protocol’s Black Iron Prison and eventually make it to the exit. However, an infected and still coherent Captain Ferris ambushes them and launches them out into the cold exterior of Callisto, with Elias tragically dying in the process.
Jacob Teams Up With Dani To Escape Black Iron Prison
Shortly after Elias’ death in The Callisto Protocol, Jacob meets up with Dani again, and she begrudgingly agrees that they need to work together to survive. They repair a transport vehicle that can take them to the hangar, where they can commandeer a ship for Jacob to fly them away from Callisto. However, Dani takes them on a detour to Jacob’s crashed ship. They go through the remains until Dani finds the cargo Jacob was hired to bring to Callisto. She reveals that she tracked him from Europa because she had reason to believe that he was transporting biochemical weapons used in the attack on Europa, which he experiences with the CORE device during The Callisto Protocol’s terrifying gameplay.
Jacob opens the cargo container for Dani, revealing that it only contains medical supplies. Dani is puzzled by this, having sworn by her leads, but comes to have more trust in Jacob. With the matter settled, the pair travel to the hangar and prepare to steal a ship on a landing pad. However, Duncan Cole, the warden of Black Iron Prison, appears via hologram and addresses the two. He suspiciously knows a great deal about their backstories and says he cannot let them escape, as an experiment he calls The Callisto Protocol is not yet complete. Warden Cole shoots down the ship, which then crashes into the hangar building, sending Jacob and Dani into the depths of the moon.
Warden Cole Is Behind The Outbreak On Europa & Callisto
In the final, gory chapters of The Callisto Protocol, Jacob and Dani find themselves deep within Callisto in an abandoned colony called Arcas. With their escape attempt foiled, they now set their sights on getting answers to the outbreak and Warden Cole’s enigmatic statements. Dani decides they have to return to Black Iron Prison, but they first have to make it through the horrors of Arcas, which entail infected monsters stronger than the ones they came across earlier. Before it was abandoned, Arcas was a mining colony. When harvesting Callisto’s resources, miners discovered a massive worm-like alien. They shot it on sight, killing it almost immediately.
However, multiple larvae creatures still lived within and eventually latched onto the miners, infecting all of Arcas and turning them into the same creatures, which rival the scariest of Silent Hill's monsters, Jacob fought in Black Iron. The backstory is conveyed to Jacob via a locational memory triggered by his CORE implant. It features Dr. Caitlyn Mahler, head medical officer at Black Iron, recounting the alien’s discovery and her research into the infection. Mahler found similarities to another infection incident that occurred somewhere called Paramo. The infection is a kind of accelerated evolution, which Mahler believes could be harnessed with further study. Black Iron Prison was formed to act as a site where new pathogen strains can be tested.
Jacob also discovers a cargo container precisely like the one he delivered to Europa and was meant to deliver to Callisto. This is when he realizes that he is complicit in the Europa outbreak. Mahler reveals that The Callisto Protocol’s Europa colony was a testing ground for this Biophage pathogen and was ultimately successful because one individual survived the outbreak, known as Subject Zero. After studying the body of Subject Zero, Warden Cole was pleased with the outcome and wanted to unleash it in Black Iron as soon as possible so they could find a new survivor they would call Subject Alpha.
Warden Cole’s Secret Organization Is Callisto Protocol’s True Threat
Shortly after Jacob learns the truth about The Callisto Protocol’s Biophage outbreak, Captain Ferris, revealed to be Subject Alpha since he survived being infected, shows up to confront Jacob. Jacob manages to hold off Ferris for a while until Dani arrives to help him escape. As Jacob was dealing with Ferris in Callisto Protocol’s up close and personal combat system, a larvae creature attached itself to Dani, infecting her with the Biophage. She quickly falls victim to the pathogen and wants to give up, but Jacob refuses and vows to find her a cure. At that moment, a Black Iron robot arrives and incapacitates Jacob, throwing him back into his cell in the prison.
Dr. Mahler then communicates with Jacob via the CORE device, telling him that she no longer believes in the ethics of their experiments and can help him and Dani, whom she is taking care of in her lab. Jacob eventually reaches Mahler’s lab after fighting through the horror of The Callisto Protocol’s Black Iron again, where she tells him that she can synthesize a cure with a sample taken from Captain Ferris, who is likely to be found at the Warden’s office. When Jacob arrives, he finds Cole speaking with three masked figures whose holograms are illuminated on the walls. Cole and these individuals form a secret society called Kallipolis and are the actual threat in The Callisto Protocol.
Jacob Stays At Black Iron Because Of His Guilt
Cole sends Captain Ferris to attack Jacob to prove that Subject Alpha is the next step in human evolution. After a rigorous fight, Jacob defeats Ferris and uses Mahler’s syringe to make a cure. Cole tries and fails to persuade Jacob to give the cure to him to make more developments of the Biophage, another twist in The Callisto Protocol’s sci-fi horror story. Jacob cures Dani, who then tries to kill Cole, but he isn’t physically present in the room and is merely a hologram. Then, Cole activates Black Iron’s self-destruct sequence to cover up the outbreak. Jacob and Dani rush to the escape pods only to find one remaining. Jacob throws Dani into the pod despite her protests.
He is guilty of his role in the outbreaks and determines that he belongs here in Black Iron. The pod launches and Dani discovers that Jacob gave her a tube containing the Biophage so she could use it as evidence of what transpired on Europa and Callisto. After Dani safely escapes, Jacob continues to fight the monsters on Black Iron when Mahler appears to him via hologram, citing that she has found a way for them to escape and that she’ll need his help. The Callisto Protocol sequel-ready ending has a final scary note as Captain Ferris screams through the hologram.
The game is slated to release a story DLC scheduled for Summer 2023, which can show how Jacob and Mahler escape Black Iron. Without that, however, The Callisto Protocol ends on a massive cliffhanger that sets up future story potential that can be realized in a sequel.
