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The Callisto Protocol Ending Explained

One of the most hyped games to come out at the end of 2022 is undoubtedly "The Callisto Protocol," a survival-horror action game directed by "Dead Space" co-creators Glen Schofield. The game brings players to the frigid and nearly desolate moon of Callisto, where freight transporter Jacob Lee is thrown into Black Iron Prison. Not too long after being led to his cell, Jacob finds himself in a horrifying nightmare when a mysterious outbreak turns those infected into vicious monsters. At first, it's easy to see "The Callisto Protocol" as a simple homage to "Dead Space," but it makes its own unique impression.


While early reactions to "The Callisto Protocol" were a bit all over the place, it does boast its own original sci-fi horror story full of tense moments and unexpected terror, especially in that finale. 

The final act of "The Callisto Protocol" features plenty of wild revelations and stunning twists that can be a little overwhelming to absorb all at once. What becomes of Jacob and Dani by the time the credits roll? It's time to connect the dots and delve into everything that happened in the wild third act of "The Callisto Protocol."

Beware of spoilers ahead for "The Callisto Protocol."

The source of the infection

Just as Jacob and Dani search for a new escape route after Warden Cole shoots down their only chance off Callisto, they stumble upon a forgotten colony underneath the prison — and the source of this disgusting nightmare. Jacob and Dani find themselves traversing a mining colony called Arcas that existed before Black Iron was built and eventually come across a futuristic-looking lab. Upon entering, Jacob is guided by holograms of the mysterious Dr. Mahler and learns a little more about Arcus and the gigantic alien in the center of the lab. 


As explained by Mahler, miners in Arcus discovered this massive alien and were the first to become infected by this plague. After the UJC (the company that employed Jacob) discovered the alien and the infection, they initiated an operation to exterminate the colonists and cover up what happened. The plan became to extract the alien larvae and start experimenting to learn their effects on humans, resulting in the creatures called Biophages. Like many great sci-fi stories, simple human greed led to the Biophage tragedy.

What really happened on Europa

"The Callisto Protocol" opens with an outbreak occurring at another colony on Europa, and the details of that event are constantly evolving and being uncovered throughout the game. Mahler reveals that the outbreak was partially due to the UJC accidentally exposing the larvae they extracted to the public. The ensuing carnage would have lasting ramifications that would inspire both Warden Cole and Dani to take action.


As seen in a flashback moment in which Jacob merges with Dani to see her memories on that fateful day, Dani lost her sister during the outbreak, which spurred her on to stop Cole and lead a rebel faction known as The Outer Way. 

As for Cole, the story of a supposed "Subject Zero" — an infected human who was able to retain their humanity before being killed by security — is what really struck him. His interest in replicating this incident is what initially got him interested in this alien virus. It also ultimately leads to the Black Iron outbreak and the main events of the game.

Confronting Cole

After seeing Cole's holograms all over Black Iron and learning that he destroyed the only possible means of escape, Jacob is finally able to confront Cole in-person, at which point he learns a lot about him. Upon entering the room, Jacob sees Cole talking to veiled members of The Commonality, the cult sect that Mahler says Cole is a part of, before giving his big villain speech. In short, Cole talks about how he believes that this virus will help achieve The Commonality's goal of advancing human evolution. 


Cole further states that his "Subject Alpha" will be the prime example of the virus' benefits and that there's nothing that Jacob can do to stop anything. It's basically the famous last words any "Resident Evil" fan has heard from one of that series' villains before, usually right before the final boss fight. 

That's exactly the case here, as it leads to a final confrontation between Jacob and a mutated Ferris, the head of Black Iron's security and Cole's Subject Alpha. However, there's something that remains mysterious about Cole: Not only is he projecting a hologram and decidedly not at Black Iron, but his role in The Commonality raises many more questions. 

The Commonality

The Commonality are easily the biggest mystery that "The Callisto Protocol" leaves hanging, but there are some things we know about them. For instance, Mahler explains that Cole is a key member of the group. Furthermore, the outbreak at the prison was caused when Cole enacted the titular Callisto Protocol, a plan to test the infection on the prisoners and hopefully find his Subject Alpha. It's a revelation that truly defines Cole as a disturbing antagonist, but confronting him only shows him to be even more despicable. 


As Jacob talks with Cole in his office, the villainous warden explains that he and The Commonality wish to further human evolution so that they can explore deep space and beyond. They believe this virus could be the key to achieving their goals and they're basically willing to do anything and kill anyone to make it happen. While Cole is the big focus here, it's very possible that future games in the series could focus on The Commonality becoming a clearer threat. 

At the moment, there isn't much else known about the cult, but players going for "The Commonality" achievement/trophy could uncover more. The trophy tasks players with finding secret rooms for the cult around Black Iron, which leads to plenty of small hints for fans to theorize about. 


Was Ferris a worthy subject?

Ferris is one of the game's most terrifying threats, boasting a domineering presence even in his human form. Once Ferris is shown to be infected though, he doesn't turn into a simple monster like many others and seems to retain his humanity. His vicious personality still remains, though, and he's become even more of a daunting physical threat due to his enhanced abilities. Cole even dubs him as the sought-after "Subject Alpha," so it's worth questioning if there's really something special to Ferris. 


Truthfully, Ferris can only fend off the virus for so long and eventually succumbs to the same fate as everyone else. During the final boss fight, Ferris feels himself starting to mutate again and he finally loses control of his body. Suddenly, in one of the creepiest moments in "The Callisto Protocol," his body transforms and evolves into something truly monstrous, making for one fearsome final boss. Although Cole believed that Ferris could've been the perfect test subject that he'd been searching for, this ends up just being another one of his delusions. No matter how much Ferris or Cole believed they could control the infection, neither of them met their goals.

Finding the cure

Dani's infection changes everything for Jacob in the last stretch of "The Callisto Protocol" and he refuses to escape without curing her first. However, since no one has survived after being infected, the chances of success seem pretty low. However, Mahler offers a possible cure: if Jacob can extract the DNA of Subject Alpha, he can inject it into Dani and possible counteract the virus. When Jacob faces Ferris in the final fight, he is able to get what he needs to possibly cure Dani.


After nabbing the DNA in gruesome fashion, Jacob wastes no time in injecting Dani with it and her symptoms seem to clear up almost immediately. All the gross veins running throughout her face and eyes start to dissipate and she regains her motor control and strength. Thus, Dani seems to be fully cured of the infection and is quite possibly its first survivor. Armed with this new knowledge, it's possible that they can save others who are infected, maybe even find a way to mass-produce it and thwart The Commonality's plan to expose more people. 

Jacob's inaction

For most of the game, Jacob seems simply like an innocent protagonist who was unluckily sucked into this nightmare. However, after exploring Dani's memory in Europa, players come to understand something a little more horrifying about Jacob's connection to the outbreaks. Before Black Iron, Jacob was just a simple freight transporter for the UJC and delivered different cargo to different planets, typically without much concern for what he was carrying. 


Late in the story, it's revealed that he was actually transporting vials containing the infectious larvae for the UJC, meaning he is partially responsible for the outbreak at Europa. Normally, it would be easy to give Jacob the benefit of the doubt and say that he didn't really know what he was carrying. However, as shown in the opening scene and the flashback to it, Jacob often ignored what he was carrying as long as he got a paycheck. This willful ignorance led to the deaths of many on Europa, including Dani's sister. For most characters, their actions define them. For Jacob, his inaction makes the biggest impression — and it's certainly not a heroic one. 

A final sacrifice

Cole activates a self-destruct sequence just as Jacob and Dani discover that he's actually a hologram, and our heroes find themselves in an intense race against time to get to the last escape pods. As fate would have it, there's only one escape pod left when they arrive, meaning that one of them would have to stay behind. Without hesitation, Jacob shoves Dani into the escape pod along with proof of what Cole is doing, ultimately deciding to sacrifice himself for her survival. 


This feels like a fitting way for Jacob's personal arc to close out and acts as a good redemptive moment for him. It's also a fitting moment for Dani, since she's been so determined to not only expose the experiments and stop this infection from continuing, but also to avenge her sister's death. It's always sad to see the protagonist of a game go out on a sadly sacrificial note, but Jacob's choice earns him some points for heroism and adds emotional weight to the final moments of The Callisto Protocol. But, is it really the end for Jacob?

Going down with the ship

Mahler is hidden away for most of the game and only seen in holograms, but she directly contacts Jacob when he's thrown back into his original jail cell. Upon meeting her, Jacob gets all the information he needs to have a better understanding of the outbreaks and how to cure Dani. Up until the events at Black Iron, Mahler had willingly worked alongside Cole and the UJC in experimenting with the alien larvae, in turn causing a lot of damage and death. 


However, after meeting Jacob and seeing what's happened at Black Iron firsthand, it seems she's had a change of heart. However, that doesn't mean she feels like she deserves to escape. When Jacob asks what she's going to do, she says she belongs at Black Iron, realizing that she might deserve whatever fate she suffers here. Things seemed like they would end there, but her reappearance in the final moments of the game suggest that she could have a bigger role in a potential sequel. She stops Black Iron's self-destruct sequence and tells Jacob that there could be another way out, suggesting that Mahler might be able to find greater redemption in helping Jacob escape or completely stop this nightmare for good. 


Is it really real?

Although Jacob's decision to strand himself to save Dani would make him seem like a dead man, he somehow isn't just snuffed out in the final moments of the game. As the self-destruction rapidly approaches and a wave of infected prisoners charge at him, Mahler stops the self-destruct sequence and hints that there's another way off the planet. Unfortunately, this moment of hope is almost immediately broken up by Ferris reappearing for one last scare. 


Now, this might seem like a pretty definitive ending for the game, but one can't help but wonder if these final moments are real or not? Are they just a part of some dying dream, or just a case of Striking Distance wanting to deliver one last little jolt before rolling the credits? 

Given the state we saw Ferris in after the final boss fight, it's a little difficult to believe that he would just revert to a slightly less mutated form. Plus, if Mahler knew of another way off of Callisto, why wouldn't she mention it to Jacob sooner? These could be hints of a possible sequel route, but there's still something odd about these final moments, something that makes the ending feel like it might be more fantasy than reality. 


Will there be a sequel?

There has yet to be any official announcement of a sequel "The Callisto Protocol." Given the game's mixed reception on launch, it's tough to say if a sequel being made is a certainty. Still, there are plenty of routes that a sequel could take in expanding the story. 


With Dani escaping from Callisto, a sequel could easily follow her efforts in exposing Cole and The Commonality and battling another outbreak in the process. Given the way that Cole and The Commonality act as larger than life villains, there's definitely potential for them to be explored more as franchise antagonists, particularly in a sequel that can now expand on their lore and backstory. 

Plus, the game's final moments are actually real, then a follow-up could easily see Jacob working with Mahler to find a way off Callisto while Ferris continues to hunt him down. Who knows, maybe Jacob could uncover more secrets about Cole and the Arcas as he looks for a quick escape, offering another opportunity to expand on the first game's potentially rich lore.