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The Callisto Protocol ending explained

The Callisto Protocol ending raises more questions than it answers, unveiling the true motive behind the biophage outbreak while teasing a sequel

The Callisto Protocol ending: Jacob, covered in sweat, blood and dirty, wearing his power armour as he confronts Dr. Mahler.

There’s a lot going on in The Callisto Protocol ending. Your journey through Black Iron prison has been hampered by setback after setback, but once you finally claw your way out of the depths, the plot is like a runaway train. So if you need the Callisto Protocol ending explained, have no fear – we’ve broken down those final moments, laying out the truth behind the biophage.

Specifically, our Callisto Protocol ending explained guide focuses on the latter half of ‘Tower’, the final chapter of one of the best horror games of 2022. Suffice it to say that there are major story spoilers below, so turn back now if you’re not quite ready to uncover the secret at the heart of Callisto.

The Callisto Protocol ending breakdown

As Dani slowly succumbs to the biophage in The Callisto Protocol ending, Jacob rushes to find some kind of cure. His only hope lies with the mysterious Dr. Mahler, who’s taken Dani to the secret lab at the heart of the prison for treatment. Once Jacob convenes with them both, Mahler links Jacob’s and Dani’s CORE while explaining that the only way to synthesise a cure for Dani is to take a sample from Cole’s Alpha.

Mahler then goes on to spell out the Callisto Protocol in full. During the initial outbreak in Arcas, a colonist successfully achieved symbiosis with the biophage. This ‘Subject Zero’ was killed during the sterilisation and became the basis for the Callisto Protocol, in which Warden Cole and his shady cabal attempt to recreate Subject Zero as Subject Alpha.

Additionally, through Jacob’s and Dani’s connection, we finally see the truth behind the incident on Europa: there was no terrorist attack. The biophage had been transported to Europa by Jacob and Max on the UJC Charon, as a test before the project began at Black Iron. Worse still, Jacob had discovered the alien larvae and dismissed them, leaving him responsible for the ensuing massacre – and for the death of Dani’s sister, Lili.

The Callisto Protocol ending: Jacob confronting Warden Cole and the Kallipolis figures in the conference room.

This revelation imbues Jacob with new strength to find a cure for Dani and correct his wrongs. He breaks into the conference room at the tower’s pinnacle to finally face Warden Cole, Black Iron’s pragmatic overseer. Cole converses with three masked figures projected onto the conference room’s walls, who greet Jacob with the phrase “Vir Solitarius”, or Lonely Man.

Cole explains to Jacob that the Callisto Protocol isn’t about death but ensuring that humanity can survive in the far reaches of space. According to Cole, the biophage is the next evolutionary step, and he decides to put it to the test with a contest between Jacob and his Alpha subject… who is revealed to be none other than Ferris (who else?).

Jacob and Ferris duke it out, and despite Ferris’ horrifying transformation into a hulking behemoth, Jacob emerges as the victor. He extracts an Alpha sample from Ferris, which Cole proclaims is the culmination of his work as a successful integration of humans and biophage. Heedless, Jacob injects it into Dani, who immediately begins to recover from the effect the biophage had on her.

As Jacob and Dani gather themselves, Cole leaves a tantalising crumb of a potential sequel: the data gathered during the final showdown between Jacob and Ferris will initiate phase two of the Callisto Protocol. After a wry farewell, Cole’s hologram disappears, and the reactor core’s self-destruct sequence is initiated.

The Callisto Protocol ending: Dani strapped into the escape pod, looking at the evidence that Jacob has left her in order to expose the secret of Black Iron and Kallipolis

Jacob and Dani sprint to the escape pods, only to find only one left. Jacob bundles Dani into it despite her protests, explaining that this is a way for him to face what he did at Europa. As Dani’s escape pod jettisons from Black Iron prison, Dani’s CORE completes its data transfer between it and Jacob’s CORE. She also discovers that she holds one of the larvae that Jacob had been transporting, granting her everything she needs to expose the truth of Europa and Black Iron.

While Dani wishes Jacob finds some peace in death, it’s not to be. Jacob is still alive, and Black Iron’s reactor has stabilised. He’s approached by a hologram of Dr. Mahler, who explains that there’s still a way out… but she needs Jacob’s help.

It’s an abrupt ending, but fear not: Striking Distance has confirmed that story DLC is coming as part of the season pass, scheduled for summer 2023. For the time being, however, we can only speculate on what’s likely to come next. The shadowy organisation known as The Callisto Protocol Kallipolis clearly aren’t going to sit back and wait for Dani to spill their secrets. As for Jacob, we hope that whatever Mahler has in store can bring him closer to redemption – and a nap.

Roll credits, because that’s The Callisto Protocol ending! If you’re curious about our thoughts, our Callisto Protocol review digs into some of the sci-fi horror tropes keeping the plot afloat. We’ve also got a list of the Callisto Protocol weapons and their locations and our top picks for the best Callisto Protocol upgrades that’ll serve you well in new game plus. If you’re curious about how your playtime fared against the average, take a gander at our guide that answers the question: “just how long is The Callisto Protocol, anyway?” Finally, if you’re reading this because you want to know the story but you don’t plan on playing The Callisto Protocol yourself, our list of the best PC games will have something for you to tackle next instead.