The Callisto Protocol Ending Explained – Does Jacob survive Black Iron Prison?

The Callisto Protocol Plot Synopsis

The plot is pretty straightforward and starts with freight transporters, Jacob Lee and Max Barrow. When the pair are boarded by a fugitives, fronted by a woman named Dani, the ship crash-lands, Max is killed on impact and Jacob finds himself thrown into the bowels of Black Iron Prison on Jupiter’s moon, Callisto.

Unfortunately, everything goes to hell when Jacob awakens, with monsters lurking about and the whole place on the verge of collapse. Jacob is forced to try and escape before the monsters attack and kill him.

What is happening in Black Iron Prison?

A fruitless visit to Jacob’s ship with Dani brings new frustrations. Dani is adamant that Jacob brought bioweapons onto the planet, but she only finds medical supplies in the cargo hold (We’ll come back to this don’t worry!)

The pair soon wander through Callisto’s original colony, built underneath what is now Black Iron Prison. The UJC exterminated the entire colony and covered up what was going on. The Arcas miners had accidentally unearthed a dead alien creature with thousands of larvae inside it.

Seeing the potential for accelerated evolution, the UJC decided to harvest this larvae and experiment on humans, which ultimately caused the outbreak on Callisto and at Black Iron Prison.

What’s happening to Dani?

Captain Ferris ambushes Dani and Jacob after exploring the depths of the prison. Although Jacob manages to stop the mutated Captain, scrambling into an elevator in the process, Ferris manages to infect Dani with the biophage, setting up a ticking timebomb of disastrous proportions. Jacob is on a tight window and forced to try and find an antidote before it’s too late.

Believing the answers are at Black Iron Prison, Jacob tries to enter but is unfortunately knocked out and thrown back in his original cell by the security robots.

How does Jacob escape his cell?

Jacob is thankfully freed from his cell by prison doctor, Dr. Caitlyn Mahler. She guides Jacob through to her lab, where she claims to be able to cure Dani’s infection and get him the Warden, Duncan Cole. Mahler has taken Dani to her secret lab, deep in the heart of the prison. This doctor is also the same one who inserted the Black Iron chips into Jacob and Dani originally.

The only way to save Dani is to extract Ferris’s DNA, Duncan’s “alpha” subject, which can be used to synthesize an antidote. She provides Jacob access to Dani’s memories through their neural implants, which brings up the real truth over what Jacob has kept concealed all this time.

What is Jacob’s secret?

Thanks to Jacob’s new neural link, he learns that Dani’s sister was killed in the Europa outbreak, and he was instrumental in this occurring. It turns out the UJC was using his ship to smuggle alien larva samples all this time. Jacob became aware of this but decided to stay quiet, driven by greed given the payments he was receiving.

What is The Callisto Protocol?

When Jacob finally catches up, the Warden explains that the Callisto Protocol was an experiment to recreate the original Alpha. Duncan is the one who ordered a second outbreak to occur in the prison, similar to that with Arcas. He wanted to find a subject compatible with the alien infection, his “Alpha” as it were. And Duncan Cole appears to have found that in Captain Ferris.

After a fight with Warden’s new Alpha, Jacob comes out victorious and extracts the DNA he needs. The Warden tries to convince Jacob to turn it over to him but Jacob refuses. Dani shows up and fires several bullets at Duncan but unfortunately they phase straight through. He’s a hologram.

Jacob decides to use the antidote on Dani, curing her in the process. Angered by this betrayal, Duncan activates the prison’s self-destruct countdown and claims that he has enough data to carry out the Callisto Protocol again, disappearing from view.

How does The Callisto Protocol end?

Jacob and Dani rush to the prison’s escape pods but they’re dismayed to learn there’s only one left. Jacob puts Dani in along with an alien larva sample, giving Dani everything she needs to expose the UJC’s experiments and stop this from happening again.

Jacob stays behind in Black Iron Prison and fights his way through waves of infected creatures. All hope looks lost until Dr. Mahler contacts him again. She’s temporarily stopped the self-destruct sequence and claims they have a means of escape but need to work together. However, her hologram is cut off by Ferris, who’s seemingly still alive in his pre-Alpha form, attacking Jacob.


Read More: The Callisto Protocol Game Review

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