The Alters: Act 3 Walkthrough

Depending on the players’ choice at the end of Act 2 of The Alters, the beginning of Act 3 will present players with different challenges, though the main objectives will remain the same. The decision between using Tabula Rasa or Neural Implants will permanently change the ending of the game as well.

Do note that this guide will not discuss the different endings of The Alters but rather focuses on the main quests and side missions of Act 3 and how to complete them. Things will be slightly different based on your choice at the end of Act 2, though that decision will not affect the Interlude section.

Act 3 Main Story Questline

After coming back from the Interlude, the first thing you want to do is head to the communication room. Depending on your choice in Act 2, you will either talk to Maxwell or Agatha. No matter who you are talking to, the first objective will be to create a beacon. It is also strongly recommended that you research all available upgrades for the Luminator device early on in Act 3, as you will need to use it frequently throughout the act.

If you have enough resources (50 Metals and 50 Minerals), craft the beacon at the Workshop, but if you don’t, use the map further below to easily locate the resources and build mining outposts. Once you craft the beacon, a location will be marked with a red icon on the map. Head there and place the beacon.

Unfortunately, the beacon will not light up, as an unknown anomaly will prevent its activation. Go back to the base and speak with the Scientist about it. Initiate the Beacon Blockade research after that, and assign the Scientist to finish it as soon as possible.

In the meantime, try to make progress in the side quests or just maintain the base until you receive a call. Depending on the Act 2 choice, the person behind the call will be either Lena or Lucas.

Once the research is over, the Scientist will mark three locations on your map with pink markers. You need to reach those locations and use the Luminator device to expose the anomalies. These anomalies will be cores of light, similar to those veins that lead to Planetary Samples. Once you expose all three anomalies, go back to base and report to the Scientist.

This time around, you will need to initiate the Materializer Module in the Mission tab of the Research tree. Also, you should craft a Fragmentation Device at the workshop, requiring 100 Rapidium, 50 Metals, and 50 Minerals. In between, a new call will also be available from Lucas if you have taken the Neural Implant path earlier.

Once the research is over, go to the Base Building menu and construct the new Materializer Module. Talk to the Scientist once more, and he will set you up on a mission to ignite the Materializer and climb up the anomaly tree. But, before you do this mission, it’s best to upgrade the Luminator device as many time as possible.

Also, it’s strongly recommended you craft some Radiation Shields and Suit Batteries for your suit before starting the mission.

As the quest itself suggests, it’s best to begin this mission earlier in the morning. The mission’s location is marked with a pink marker known as Tree Entry. Head there to initiate the mission.

This mission will task you with climbing up a tree, which will require the player to use the grappling hook multiple times, and that needs to be recharged later in the mission. Due to the nature of the mission, the suit will charge automatically over time, but using Suit Batteries will be a lot faster and easier, as the recharge rate is quite slow.

Moreover, the path to the head of the tree is filled with radiation anomalies, and while you can dodge some of them, using Luminator will be mandatory to go through some parts of the path without absorbing a large amount of radiation. Using Radiation Shields, however, can provide more room for mistakes.

Once you reach the top of the tree, there will be three anomalies with a blue ring surrounding them. Use the Luminator to wipe out these anomalies and a crystal-like shape will appear. All you need to do now is to place the Fragmentation Device at the foot of the Crystal and then head to the tip of the tree and jump down.

The top of the tree will be full of radiation anomalies, which can be melted down by Luminator to turn them into ALX.

Knowing that you can refine ALX into Minerals by some research, it’s actually worth it to melt the anomalies and collect some resources if you have enough time. Minerals will be required in the upcoming crafting to end Act 3.

After completing the mission, return to base and skip to the next day. In the morning, every alter will be in the kitchen. Meet the alters and talk about the possible ways to smuggle them onto the rescue ship. At the end of the meeting, head out to the beacon’s location and activate it. Now, multiple tasks will be available with yellow font. While you are only required to tackle one task from each quest, it’s best to complete all these tasks if you have two or three days until sunrise. This way, you will get all the options for different endings, and you can just load your last save before making your final decisions to see how they affect the ending.

The first thing you need to do is to initiate three new research studies: Ark Sarcophagus, Suit Mask, and Autopilot Device. In the meantime, Lucas will call, asking the player to craft a device known as RAT. So, head to the workstation and craft the following items: Sleeping Gas (10 Minerals and 120 Organics), 4x Explosive Charges (40 Minerals and 160 Organics), and the RAT device (10 Metals and 40 Minerals).

Keep in mind that once the research studies are done, you will need to craft Suit Mask Upgrade and Autopilot Device at Workstation. Moreover, you should add the Ark Sarcophagus module (30 Metals and 40 Rapidium) to the base in the Base Building menu.

Don’t worry if the mass of the base exceeds the Organics storage, as the base is not supposed to move anymore.

Once you have completed all the missions that are tagged with a yellow font, everything is ready for the finale. Head to the navigation system’s monitor and click on Proceed. But keep in mind that this is a point of no return. If you want to complete any side quests, make sure to do them before initiating the navigation system; otherwise, they will fail.

After the navigation system is initiated, everyone will gather inside the Ark Sarcophagus. Meet all of them and say goodbye to them. If you have Botanist in your team, he will ask to swap places with you. If you accept this offer, you will get one of the Botanist endings. Otherwise, you will get one of Jan’s endings (depending on your other decisions).

Once everyone is inside the cryosleep, go to the Airlock and head out. You will meet the rescue team, and your dialogue with them will not have any effect on the outcome of the story. However, once your character (either Jan or Botanist) reaches the rescue ship, you will get some options based on the yellow-marked quests that you have completed. The first decision is about how you treat the rescue team members.

You can detonate the explosive charges to kill them all, you can plant the sleeping gas inside the ship to make them unconscious during the trip, or you can do nothing. The final decision will be in favor of Maxwell or Agatha, as that is what they would want you to do.

If you don’t choose “Do Nothing,” the next decision that you make is to either use your own Autopilot device or use Lucas’s RAT device. The involvement of Lucas in stealing the rescue ship will also affect the ending.

Depending on your decisions, Act 3 will wrap up, and you will get to see the outcome of your decisions in the Epilogue, which has no gameplay.

As mentioned earlier, this guide will not go through the difference between endings, as you can check them out in its dedicated endings article.

Act 3 Side Quests

Similar to previous Acts, there are a number of side quests available in Act 3 as well. Completing these will change the fate of some of the alters, especially if you have proceeded with the Neural Implant solution back in Act 2.

The Aftermath

Choosing either of Tabula Rasa or Neural Implants to cure the alters at the end of Act 2 will cause some of the alters to leave the base. This side quest is about finding the rebels and convincing them to come back to base. If you have chosen Tabula Rasa, the alters will never come back to the site again, but this mission will still be available.

This requires the player to find the camp of the rebels. To ease your job, the location of the camp is marked on the map above. Get there and talk to the Technician, who is the head of the rebels.

Head back to the base now and craft a Supply Package at the workshop. Now, deliver the supply package to the rebels. If you have chosen the Neural Implants earlier, this package will convince the rebels to come back to the site.

Imagine Sisyphus Happy

If you have Doctor on your team, he will request to talk about a subject after crafting the beacon. The Doctor will ask Jan to try and restore his tattoo. Now, the player should speak with other alters about the tattoo, especially the Scientist.

After that, a tattoo machine will be craftable in the workshop. Create it and then put the tattoo machine in the Infirmary module. Then, speak with Doctor again and take him to the infirmary. Based on who you have talked to about the tattoo, you will be given some options. But the Artistic Design is the best for the Doctor.

Once the tattoo is restored, he will be happy with the result, and the quest will wrap up.

Every One Counts

This is a repeating side quest coming from the previous act. It will only complete when Jan manages to build five Rapidium Arks in the base. It’s worth noting that completing this side quest will have a slight impact on the game’s ending.

Meaning of Life

In the final days of Act 3, the Scientist will request for a talk with Jan. He will ask to leave the base and spend some time outside. If Jan agrees to the request, he will be gone from the base for 24 hours, and all research studies will be halted for the time being.

The next day, the Scientist will return to the base again. When Jan talks to him, the Scientist will reveal a new location on the map, asking Jan to check out his new discovery. The player should visit the location, which seems like a lost haven on the planet. Now, return to the base, and speak with the Scientist once more.

The Scientist will reveal his willingness to stay on the alien planet rather than return to Earth. However, the final decision must be made by Jan. If the player lets the Scientist pursue his dreams, he will leave the base after five days and will not join the other alters to be smuggled to Earth. Allowing the Scientist to stay will tick the quest and unlock Hidden Truth achievement.

Saving Ben

This quest will only trigger if you have Refiner in the team. Somewhere in Act 3, Refiner will have a talk with Jan about Ben and his doomed fate. If you have chosen Neural Implants at the end of Act 2, you can indeed save Ben.

When Lena calls you, speak with her about Ben’s situation, and she will make sure to rescue Ben from the explosion. The next time that Lena calls, she will inform Jan about Ben and the fact that he is safe now. Reporting the news to the Refiner will complete this quest.

Players who have chosen Tabula Rasa earlier in Act 2 will not be able to save Ben, as the explosion will kill him eventually. However, the player can decide to either let the Refiner know about this or hide the news from him.