Here you'll find an outline of The Callisto Protocol's story and plot summary. Read on to learn about everything that has happened in the Black Iron Prison, the alleged terrorist bombing in Europa, as well as Jacob's journey as he tries to escape Callisto!

Main Story Walkthrough

Story and Plot Summary

The Callisto Protocol Story Setting

Takes Place on Jupiter's Moon

Our story takes place on Callisto, one of Jupiter's moon orbitting the planet. On it, the United Jupiter Company, has built the Black Iron Prison, a maximum-security holding facility. Beneath this monstrous prison, lies an even darker secret.

The Callisto Protocol Story and Plot Summary

Just Another Supply Run

Our story begins with a news update of a terrorist attack on the moon Europa caused by the terrorist organization Outer Way led by Dani Nakamura. Our protagonist Jacob Lee is en route with his first mate Max Barrow on a standard supply run of medical supplies from Europa to Callisto, the prison moon of Jupiter. After a short talk with Max regarding the job, Jacob decides to check on their cargo.

Being Boarded

Jacob finds that their ship has been boarded by The Outer Way terrorist group. He tries to sneak past the interlopers and back to the cockpit. The Outer Way catches up to him and Dani Nakamura shoots the door causing the ship to crash on Callisto.

Crashing into Callisto

Jacob tries to fly what's left of the ship and safely land it in Callisto in one piece. After the crash, he awakes to find that his first mate Max is dead. He is then saved by security personnel and then escorted to the Black Iron Prison by order of the Warden.

Becoming Inmate 532-521

Jacob is held against his will, forced to undergo registration and processing as inmate 532-521. Dr. Caitlyn Mahler implants a CORE device in Jacob's nape, the standard for prison personnel and inmates.

Haunted by the Past

Jacob wakes up from a dream after seeing a mysterious cube and getting attacked by Max's dead body. He now finds himself locked in a cell and the entire prison is in chaos.

Meeting Elias

Jacob finds another inmate, Elias Porter, and agrees to help him in exchange for an opportunity to escape Black Iron Prison. Jacob finds the control room for Elias' cell and frees him. They agree to meet up in a safe room in the watchtower.

The Death of Cpt. Ferris

The only obstacle left between Jacob and Elias is Cpt. Leon Ferris up on the Security Main Control Room. Jacob uses the blast door as a shield, and unleashes biophages on Cpt. Ferris leading to his untimely demise.

Reuniting with Elias

After getting to the safe room Elias had promised, Jacob is given a BI-55 Hand Cannon model to be reforged. Elias tells him that they need to free another prisoner who has the connections necessary for getting off Callisto. The catch is that they're being held at the SHU, a separate holding unit accessible only via gondola.

Infiltrating the SHU

Jacob meets up with Elias in the SHU Command Room. Jacob gets on the gondola and infiltrates the SHU to look for the inmate Elias promised. After many encounters with Biophages, Jacob arrives at Cell Wing A to free the last person he wanted to see.

Freeing Dani

He learns that Dani Nakamura, the leader of the terrorist organization The Outer Way, is the person he was meant to save. Dani is untrusting towards Jacob, holding him responsible for what happened in Europa and what was happening in Callisto.

Escaping Black Iron Prison

After managing to escape the SHU Station, Jacob catches a glimpse of the outside world. The Tram Station is location inside the giant dome, but to reach that, Jacob must go underground.

Jacob must pass through the Water Processing facility as he tries to evade as many Biophages as possible. At the end of the facility lies the ladder that will lead him straight to heart of the dome

To the Tram Station

After surviving a waterslide and biophage-infested cavern, Jacob finally arrives at the Tram Station. Elias asks him to make a detour in Oxygen Processing to lift the lockdown protocols. Elias advises him to take a detour in Utility to account for the collapsed walkway.

Ferris' Phantom

After reuniting with Elias and suiting for the surface, an infected Ferris blasts the airlock sending Jacob and Elias to be sucked out of the facility and onto the moon's surface.

Escaping Callisto

Jacob wakes up in the middle of nowhere in a storm. He hurries to find Elias close to death. Dani later shows up and retrieves Elias' implant bios to gain information on how to get off Callisto. Still untrusting towards Jacob, Dani refuses to take Jacob in the Snowcat but instead points him in the direction of the Hangar.

To the Hangar

Jacob walks towards the Hangar, but to get there he has to go underground through the Tunnel system dug up by miners. Jacob exits the tunnels by the Garage where he meets up with Dani. Dani tells him to find a way to get the main gate unlocked so they can both get out of the facility aboard the Snowcat.

Revisiting the Crash Site

After regrouping in the courtyard, Dani takes Jacob to the crash site. After denying that he had anything to do with what happened Europa, they both make their way to the Hangar.

Almost Out of Here

When they reach the hangar deck, Dani tries to get a nearby ship to land but Warden Cole overrides the anti-aircraft missile system shooting down the ship causing it to crash into the hangar. This sends Jacob and Dani flying as the hangar falls apart.

What Lies Below

After waking up, Dani learns that Arcas, the original colony, still exists. She convinces Jacob to take the Transport Hub from the Colony back into Black Iron. On their way to the colony, they get separated again as Jacob falls deeper into the tunnels.

Jacob wakes up in the presence of a new mutation of the Biophage, The Blind. A blind biophage that is highly reactive to sound. He must find a way to get power back into the Transport Platform to get to the Colony. On the transport he finds another new mutant, the Two-Head.

The Secrets of Callisto

When he gets to the Colony, he finds Dani seemingly in a trance as she downloads all the data and information from a dead miner. She tells Jacob of the events that led to this. Convinced that this outbreak was no mere accident, they venture deeper into the colony to learn the secrets of the Callisto outbreak.

An Ancient Virus

After another encounter with a Two-Head, Jacob and Dani head further into colony to discover a research lab where they extracted samples of the original virus and tried to replicate it as a bioweapon.

Dani gets Infected

Ferris shows up once more, this time slightly more mutated than the last time. After narrowly escaping Ferris, Dani gets infected with the virus. Convinced that the Warden must have an antidote somewhere in the prison, Jacob and Dani try to find a way back into the prison until they are intercepted by security droids.

Coming Back Full Circle

Jacob finds himself getting dragged back into his old cell when he hears the voice of Dr. Caitlyn Mahler. She tells him that she can save Dani with his help. Jacob then rushes to the Mahler's research lab to find her injecting a serum in Dani to hamper the progression of the virus.

A Plan to Save Dani

With the help of Dr. Mahler, Jacob learns the truth of the events that have transpired by tapping into Dani's memories. He is responsible for what happened in Europa, and what was happening to Dani. Dr. Mahler hands him an antiserum that could save Dani's life, but it requires getting a sample directly from the Warden's Alpha.

Getting the Antidote

Jacob confronts the Warden and learns that everything has come according to plan. Warden reveals that his plan of using the biophage virus to force humanity to evolve for the stars. Jacob must take down Ferris, the Warden's Alpha, if he is to save Dani.

A Price to Pay

After defeating Ferris, Jacob extracts a sample and synthesizes an antidote. He gives it to Dani just in time to save her. The Warden reveals that there is nothing to stop the destruction to come. The entire facility is now falling apart. Jacob and Dani hurry to the escape pods. Jacob makes the ultimate sacrifice by throwing Dani inside the pod, leaving him to die on Black Iron as penance for what he's done.

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