The Alters presents numerous decisions throughout its narrative. Most of these are immediate and personal, influencing the survival of the mobile base and its crew, but several key choices—particularly in the second half of the game—significantly affect how Jan's story concludes.

This guide outlines all the critical decisions you’ll face and how each one affects the epilogue once the journey ends. Sometimes a small decision can lead to a major outcome, while other endings require an entirely different playthrough to witness.

This guide contains spoilers. We recommend completing the game at least once independently before proceeding.

Rapidium

One of the first major factors affecting the ending is how much Rapidium you collect before the rescue ship arrives. You can build up to five Rapidium Arks during the campaign; one initially, and an additional one with each Base Expansion upgrade constructed. The more Arks you build, the better Project Dolly performs, which has a positive impact on Earth—most of the time.

Maxwell Versus Agatha

Throughout the first two Acts, Maxwell insists that no one on Earth must learn about the Alters. If you keep this secret from Lena (which limits you to using Maxwell’s treatment for the Alters' brain condition in Act 2), he remains your ally into Act 3. However, if Lena discovers the truth and develops neural implants instead, she reports Maxwell to the board, leading to his dismissal and forcing you to work with Ally Corporation’s COO, Agatha, moving forward.

In terms of gameplay, Act 3 unfolds similarly regardless of your choice, with one significant exception: the Technician and any other Alters who leave the base will only return if you used the neural implants, meaning that choosing Maxwell results in permanently losing those Alters. The ending sequence remains the same either way; your patron threatens you if you attempt to save the Alters by deviating from the extraction plan. You must decide whether to sabotage the rescue ship to save the Alters or allow the soldiers to proceed, ultimately surrendering them to either Maxwell or Agatha.

Maxwell's Ending

If you let Maxwell oversee the rescue mission as planned, he takes all the Rapidium you’ve gathered and uses it to revive his neuroscience experiment, Project Elah. The global food crisis worsens, and the Alters are imprisoned for testing. Lucas abandons Maxwell’s scheme and leaves to focus on humanitarian efforts, while Jan receives a new identity and a comfortable life—but under Maxwell’s control indefinitely.

Agatha's Ending

If you allow Agatha and the Corporation to complete the mission without interference, Lena is promoted to Head of Rapidium Technologies but cuts Jan out of her life after he betrays the Alters. The Corporation uses Jan as the public face of their propaganda, and the Alters vanish completely. It's implied they were killed, though Jan receives a mysterious encoded email just as he leaves his apartment, hinting otherwise—their ultimate fate remains uncertain.

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Saving The Alters

If you're willing to risk going against Maxwell or Agatha, you can save the Alters by sabotaging the rescue team, as discussed among the crew before lighting the beacon. Even if you don’t intend to save them, you still need to make the Alters believe you will by preparing for the arrival of the rescue team:

• Constructing the false Rapidium Ark.
• Crafting either four Explosive Charges or a Sleeping Gas Canister and Suit Mask Upgrade.
• Creating either an Autopilot System or, with Lucas’ help, a Remote Access Terminal.

Should You Use Explosive Charges Or Sleeping Gas? Explosive Charges are cheaper and don't require extra research. If you plant them around the base before the rescue team arrives, you can detonate them and kill the soldiers. However, doing so worsens Jan's legal consequences, adding four counts of murder to his trial.

The Sleeping Gas method takes longer, so if time is short, you may not have a choice. There is no penalty for using gas, making it the safer option. The only real reason to use explosives is to unlock an Achievement / Trophy.

Should You Trust Lucas?

If you've earned Lucas’ trust, he’ll offer to remotely redirect the rescue ship using the Remote Access Terminal. Letting him assist not only ensures a fairer distribution of Rapidium back on Earth, but also gives Jan an alibi. Lucas claims responsibility for hijacking the ship or even blames Maxwell, shielding Jan and reducing his sentence.

If you manually redirect the ship using the Autopilot System, Lucas won’t be able to cover for you, and Jan will have to include the hijacking charge in his plea deal.

The Botanist

If you're working with Agatha and have completed the Botanist’s storyline by Act 3, he’ll request a private meeting near the end of the game. If you accept, he proposes switching places at the last moment, allowing the Botanist to return to Earth as Jan Dolski while Jan Prime escapes with the Alters.

If you don’t reject the idea outright, the Botanist will always be the last Alter you speak to before the crew enters cryosleep. At that point, you’ll have the chance to swap identities, playing as the Botanist during the ending.

Betrayal If you don’t interfere with the soldiers while pretending to be Jan, the Botanist takes Jan’s place in court, revealing himself only to Lena. He secures a light sentence thanks to Lena’s influence and cooperation with Agatha, but Lena calls to ask what happened to the real Jan. Regardless of what he says, Lena figures out the deception and demands honesty, which he provides before hanging up.

Trading Places

Agatha follows through on her threat to fire Lena because "Jan" didn’t cooperate, and the Botanist speaks with Lena before his sentencing. They talk about possibly rekindling their relationship and speculate on where Jan Prime might be now.

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