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The Alters requires players to make numerous decisions throughout its narrative. Many of these choices are immediate and personal, influencing the survival of the mobile base and its crew. However, some of the significant choices, especially in the latter half of the game, play a crucial role in determining the conclusion of Jan’s story.
This guide outlines key decisions players must consider and how each affects the game’s ending. Sometimes a small choice can lead to a major difference, while other endings necessitate a full replay to uncover.
This guide contains spoilers. It’s best to complete the game at least once yourself before diving in.
Rapidium
The first significant factor that influences the ending is the amount of Rapidium you collect before the rescue ship arrives. You can create up to five Rapidium Arks during the game: one at the start and one for each Base Expansion upgrade you complete. The more Rapidium Arks you create, the more successful Project Dolly will be and the larger positive impact it will have on life back on Earth… in most scenarios.
Due to Rapidium’s unstable quantum state, only Rapidium stored in Arks survives the journey back to Earth. The total amount you’ve stored in standard storage doesn’t count—only the number of Rapidium Arks matters by the end of the game.
In nearly every ending except for Maxwell’s (which you can read about below), most of the Rapidium will end up with Ally Corporation, which hoards it for research. If you manage to bring back a significant amount, they allow licensed franchisees to innovate technology with it, reducing the global food crisis. If Lucas helps during your escape, he ensures that additional Rapidium reaches independent startups that begin addressing the food shortages immediately.
Check in with Lucas each time you create a Rapidium Ark; having him on your side by the end of Act 2 is crucial, and making Arks is essential for that. Aim to complete at least three before activating the Neutralizer Towers if you want his support later.
Maxwell Versus Agatha
In the first two acts, Maxwell insists that no one on Earth can learn about the Alters. By keeping this secret from Lena, which means relying solely on Maxwell’s treatment for the Alters’ brain problem in Act 2, Maxwell remains your supporter in Act 3. However, if Lena discovers the Alters and creates the neural implants, she reports Maxwell to the board and has him removed, forcing you to work with Agatha, the COO of Ally Corporation, from that moment on.
In terms of gameplay, Act 3 proceeds similarly under both characters, but there’s one critical difference: the Technician and any Alters who leave the base will only return if you used the neural implants. Consequently, siding with Maxwell means permanently severing ties with them. During the ending sequence, though, your patron threatens you should you attempt to save the Alters by deviating from the extraction plan. You can either sabotage the rescue mission to save the Alters or let the soldiers proceed, ultimately surrendering the Alters to Maxwell or Agatha.
Maxwell’s Ending
If you permit Maxwell to guide the rescue operation as arranged, he will take all the Rapidium you’ve collected to revive his neuroscience project, Project Elah. This worsens the global food crisis, and the Alters become subjects for testing. Lucas abandons Maxwell’s plan to focus on humanitarian efforts, while Jan assumes a new identity and a comfortable life but remains tied to Maxwell indefinitely.
Agatha’s Ending
If you let Agatha and the Corporation execute the rescue plan without obstruction, Lena receives a promotion to Head of Rapidium Technologies but cuts Jan out of her life as he betrayed the Alters. The corporation uses Jan as the public face of its latest propaganda, while the Alters vanish without a trace. Although it suggests they may have been killed, Jan receives a mysterious coded email just as he leaves his apartment, implying otherwise; ultimately, the fate of the Alters remains uncertain.
Saving The Alters
If you’re willing to defy Maxwell or Agatha, you can save the Alters by sabotaging the rescue team, as the crew discusses before triggering the beacon. Regardless of your intent to save them, you must make them believe you’re prepared for the rescue team’s arrival by getting ready:
- Constructing a false Rapidium Ark.
- Creating either four Explosive Charges or a Sleeping Gas Canister and Suit Mask Upgrade.
- Making either an Autopilot System or, with Lucas’ assistance, a Remote Access Terminal.
You can prepare every possible option, but you can only select one when the rescue team arrives. Having all alternatives ready makes it easier to load your save and explore other outcomes.
No matter how you approach the situation, neutralizing the guards and commandeering the rescue ship means Jan will return to Earth as a criminal, but it guarantees the Alters’ safety.
Should You Use Explosive Charges or Sleeping Gas?
The Explosive Charges are less expensive to make and don’t require additional upgrades for research. If you place them around the base before meeting the rescue team, you can detonate them to eliminate the soldiers. However, doing this will worsen Jan’s sentence, adding four counts of murder during his trial.
On the other hand, using Sleeping Gas takes longer to implement, so if you’re running against the game’s time constraints, you may not have a choice. But there’s no penalty for putting the guards to sleep. The mainly compelling reason to use explosives is to earn the Achievement/Trophy associated with it.
Should You Trust Lucas?
If you’ve built trust with Lucas, he will offer to guide the rescue ship to a safe location via the Remote Access Terminal. Accepting his help not only ensures fair distribution of Rapidium back on Earth but also provides you with an alibi. Lucas will claim that the idea to hijack the ship was his or shift the blame to Maxwell, helping Jan reduce his overall sentence.
If you use the Autopilot System to redirect the ship on your own, Lucas cannot cover for you, and Jan will have to factor in the hijacking when negotiating his plea deal.
The Botanist
If you’re collaborating with Agatha and have finished the Botanist’s storyline by Act 3, he will ask to speak with you towards the game’s end. If you engage, he will suggest swapping places at the last moment, sending the Botanist to Earth as Jan Dolski while Jan Prime escapes with the Alters.
If you do not dismiss the idea, the Botanist will always be the last Alter you bid farewell to when the crew prepares for cryosleep. At that moment, you’ll have the chance to switch roles, playing as the Botanist during the concluding scene.
The Botanist won’t have access to any of the dialogue choices that Jan Prime can make from Lessons Learned. Other than that and his different voice, the sequence involving the soldiers remains unchanged.
Betrayal
If you don’t take action against the soldiers while controlling the Botanist, he will take Jan’s place in court, revealing his identity solely to Lena. He’ll receive a light sentence thanks to her influence and his cooperation with Agatha. However, Lena will call him to inquire about the real Jan. Regardless of his response, Lena realizes what the Botanist has done and demands transparency, which he obliges before ending the call.
Trading Places
Agatha will follow through on her threat to fire Lena since “Jan” didn’t cooperate, and the Botanist converses with Lena while preparing for his sentencing. They talk about the possibility of a future together and wonder what Jan Prime is experiencing in his new life.
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