The Callisto Protocolis not an original plot for a horror game. A pilot crash lands on a prison planet gets thrown in jail and then has to survive a zombie-like breakout. That’s the general plot of the game and it’s good for what it is despite some cliches.
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The Callisto Protocolfeels like the pitch to a bigger franchise in many ways. The developers have a lot of ideas planned for sequels and even spinoffs with DLC. Will they ever get made, or will this be a one-and-done situation? For now, let’s go through the dangling plot threads left on the table in this spoiler-filled discussion.
6Is Jacob Alive?
In Jacob’s guilt, he feels like he needs to sacrifice himself to let Dani go. This would make it seem like, if there is a sequel, Dani would be the new protagonist to continue the fight. However, the scene shifts back to Jacob wherein he gets a call from Dr. Mahler who explains there might be a way out for Jacob still.
Soon after that call, the deformed body of Leon pops out to scream at Jacob too, as theone final jump scareof the game. Based on this, it might be safe to assume Jacob could make it off Callisto. Players might not even have to wait for a sequel as this could potentially be some DLC. Reusing the environment would be a cheap and easy way to produce content quickly.

5Will Dani Become Playable?
Even if Jacob does survive and Dani doesn’t become the sole protagonist, she could still be playable. Another DLC idea could have players go through whatever she did on Callisto before teaming up with Jacob. This campaign could be morefocused on gunssince it seemed like Dani was always heavily armed.
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This is in contrast to Jacob whose main weapon wasa stun batonfor a good chunk of his campaign. There could even be a mission wherein players investigate the outbreak on Europa. DLC plans aside, Dani seems ready to take on whatever organization Duncan Cole is running. Will she be alone? Will Jacob surprisingly show up to help her? Also, does Dani have more allies that are waiting at some resistance camp/planet for her?
4Duncan Cole And His Organization
Duncan Cole, the Warden of Black Iron Prison, was one of the most mysterious characters inThe Callisto Protocol. He appeared when Jacob was first brought into the prison as a hologram. It was pre-recorded too, so it wasn’t even real. This pre-recorded message will randomly pop up as players explore the wrecked prison. The game almost sets Cole up to be an illusion, prompting players to wonder if he is real.
It turns out he was real, in a way, as Jacob and Dani find out right before Cole shoots their escape ship out of the sky. Whether he was physically on Callisto at all is the real question. Was every encounter with him a hologram he was projecting from somewhere else or were there times when he was physically on Callisto? Where is he hiding now and what organization does he belong to? The masks his compatriots are wearing are reminiscent of the Court of Owls, which isa plot pointfromGotham Knights. That can’t be the answer but it is funny to think about.

3Did Jacob Have Amnesia?
Jacob getting thrown into prison is something he can’t fathom. He claims he is innocent throughout the game, which players are supposed to believe. When Dani confronts him about why she is mad, he still denies any involvement with the breakout. He even takes her to the medical supplies he was transporting to show them off. Dani finally realizes she was wrong, but it turns out she wasn’t. Jacob knew that there was a secret compartment in each chest containing tubes of something.
He didn’t know what these tubes were but he has suspicious that they were dangerous. This is revealed in Dr. Mahler’s lab wherein Jacob shows he knows about the secret latch. It’s not until he connects with Dani and has his flashback to Europa that the vision of Max shows Jacob the truth though. The big question then is this. Did Jacob have amnesia after the crash, legitimately making him forget about the secret vials, or was he playing coy in front of Dani the whole time? Something doesn’t fit these revelations which can be an issue in a lot ofplot twists in horror moviesand games.

2Jacob And Dani’s Infection Status
This next plot hole is often a question asked in horror games that have infectious monsters. TheResident Evilseries, for example, has zombies running around that can turn normal people into fellow zombies with a scratch or a bite. It doesn’t seem to affect the heroes since they have magical healing herbs which creates a lot of other questions.
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Jacob can get attacked all the time inThe Callisto Protocoland walk away fine with a simple shot of healing liquid. Dani, on the other hand, gets attacked by one monster and gets infected badly. She does get cured thanks to the final confrontation in the game, but even Dr. Mahler admits that her healing syringe was experimental. Is Dani completely cured or will her infected status return in the sequel, perhaps manifesting itself into some useful powers? If Jacob is alive, is he secretly infected as well?
1The Purple Box And Illusions
The game opens up on Europa with Dani investigating the aftermath of the crisis. At the end of this opener, she sees a purple box. When Jacob wakes up in his prison cell, he sees this box as well. It will not return until after he links up with Dani and sees her memories.
Max will force Jacob to look at the box which then turns into the prototype vials as was previously mentioned. The box, for Jacob, was an illusion to hide the truth. What was it hiding for Dani though? Is there more to the box and the illusions that both Dani and Jacob see throughoutThe Callisto Protocol? Were the manifestations of Max, for example, a glitch of the system implanted in Jacob’s neck or is there something else going on? Could there be ghosts in this universe? That might be hard to fathom in asci-fi horror talebut it could be possible.

The Callisto Protocolwas released on July 05, 2025, and is available on PC, PS4, PS5, Xbox One, and Xbox Series X.
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