The Alters Walkthrough – Act 2

This Act 2 walkthrough for The Alters covers Days 31 to 52 and dives into the next phase of Jan’s journey. You’ll explore a new section of the map, face tougher environmental challenges, and expand your base all the way to Tier 4. Major milestones include creating the Doctor, uncovering the mystery surrounding Molly and the autopsy, and building the Neutralizer Towers to allow you to keep moving forward.

You’ll also create the Guard, gather resources for the third Rapidium Ark, and complete the crucial MRI scan. This act introduces the Tabula Rasa path—offering new choices with lasting consequences—and unlocks the Contemplation Room, deepening your interactions with the Alters. As you prepare for Journey 3, this guide helps you manage your team, balance priorities, and make the right moves when it matters most.

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Day 31: Act 2 Map exploration

Start your day by checking for new tasks. One of them should be “The Great Anomaly.” Head outside and locate the anomaly—it’s hard to miss. Before doing that, take a moment to assess your resources and assign the Alters to their appropriate stations.

Talk to the Alters about last night’s party to build rapport.

Once that’s done, investigate the anomaly outside. Afterward, return to the base and find the Scientist. He’ll be speaking with the Technician about mining. If you have a decent stockpile of metals, select the Metals Outpost option when prompted.

Speak to the Scientist again. You’ll now need to craft a Gravity Sensor. Go to the Workshop. The sensor requires 50 metals and 20 minerals. If you have enough, assign the Miner to start production. While that’s ongoing, take the opportunity to explore. Begin researching all exploration-related topics—they’ll become essential later, especially in Act 3.

Behind the base, you’ll find a cave with another anomaly. Entering it triggers time dilation—the more you move, the faster time passes.

Climb up the ledge nearby and mine a shallow Organic deposit. If the path ahead is blocked by rock, queue up some Drills in production. In the meantime, climb around the blockage using the adjacent ledge.

Eventually, reach the Organics field. Along the path, you’ll also encounter another rock blockage and a shallow metal deposit. Keep an eye on the workshop—if something goes wrong, such as the Miner getting injured, reassign them to the infirmary.

You’ll come across an Energy Gate blocking progress. Beyond it lies an Enriched Metals deposit.

Backtrack and take the right path. You’ll find another shallow metal deposit and another blockage.

Continue onward until you reach a steep ledge. Jump down carefully as night approaches. Once you land, head right to find an Interal vein. Farther up, there’s another Enriched Metal deposit and a strange anomaly near a “Damaged Chip.”

Before returning to base, check your map for Gravity Sensor locations. You’ll find two, but they’re currently unreachable due to ledge height.

Return to base and speak with the Miner. Then talk to the Scientist again about the new anomalies you’ve discovered.

By now, you should realize two key things: you need to upgrade your exploration capabilities (a larger battery and cheaper climbing options) and build more pylons and outposts. These were likely skipped earlier due to power or capacity constraints. Wrap up your day once everything is set.

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Day 32: The Doctor

Your goal for the day is to set up Outposts for both Organics and Metal. Start by reviewing your resource inventory and production queues. Key items to prioritize include the Qubit Chip (for research progress), Suit Batteries (to extend exploration range), Outposts (to gather essential resources), and Pylons (to maintain connectivity between modules).

Head to the Workshop early and begin crafting the Qubit Chip manually—work shifts don’t start until 9:00, so it’s a good time to get ahead. Once that’s done, upgrade the Quantum Computer.

With the upgrade complete, you can now create another Alter. Choose between the Doctor and the Refiner. Select the Doctor if you anticipate injuries becoming more frequent.

Begin your exploration by heading south. Open the Research tab and take note of the newly available options in the tree.

As you move along the southern path, expect to encounter anomalies and two steep climbs on either side. Eventually, you’ll reach a fork in the path—take the right path first.

This will lead you to an Organics Depot, where you can place your Organics Outpost. While setting up Pylons, initiate research on Metals Efficiency II to stretch your limited pylon supply while waiting for new ones to craft.

Search for a nearby Metals Deposit. If you come across inaccessible areas, queue up a Hook Upgrade in the research panel—it’s essential for advanced traversal.

To access the deposit, you’ll need to pass through an Energy Gate, which will drain your battery. Avoid or neutralize any anomalies in the area. Once clear, place the Metals Outpost.

Setting up the Pylon here may be tricky. The terrain might block a direct connection from the Hub Pylon (if you’ve researched it) to the Organics Outpost. Additionally, another Energy Gate may block the alternate long route for placing pylons, so plan carefully.

As night falls, return to base. Speak to the Technician—he’ll mention feeling unwell. Wake the Doctor to begin treatment or monitoring.

If your stamina is low, wrap up any final tasks and end the day before exhaustion sets in.

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Day 33 : Molly

Start your day by heading to the kitchen when prompted for the task “Something You Should Know.” There, you’ll learn that Molly, the sheep, has died.

Shortly afterward, you’ll need to make a decision about how to proceed. No matter your choice, it will lead to an autopsy. To keep things smooth, select “It’s a mandatory procedure. Let’s do it.”

This initiates the task “The Value of Life.” Open the Research tab and queue up the Autopsy project.

Next, review your resources and update your production queue accordingly. Assign the Doctor to the kitchen, since he provides a bonus to cooking.

Your main objective today is to complete the Pylon network for your Metals, Minerals, and Organics Outposts. Start by heading to the Organics deposit. Just above it, you’ll find a Minerals deposit blocked by rock.

Clear the blockage and place the Minerals Outpost. Then, position a Pylon to link it to the Organics Outpost, and confirm the connection on the map.

Also verify that the Organics Outpost is connected back to base. Assign Alters to begin harvesting resources while you move toward the Metals Outpost.

The Pylon setup here is more complex. Ensure line of sight between a Pylon near the Minerals Outpost and another one on a ledge overlooking the Metals area. Adjust placements as needed.

Assign Alters to all three resource stations for ongoing collection. If you’re running low on metal, gather some from a shallow deposit near the Energy Gate.

Begin researching the Hook Upgrade to access more difficult terrain.

Then move to a nearby shallow Organics deposit and continue collecting resources from the area. Once you’re satisfied with the day’s progress, end the day.

If your radiation levels are high from anomaly exposure, rest in the infirmary instead of your usual quarters.

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Day 34: Starting the Autopsy

Start the day in the infirmary, as you’ll be recovering from radiation exposure or injury. Your main goal today is to upgrade all exploration capabilities to prepare for placing the Gravity Analyzer.

Begin by focusing your research on climbing upgrades, and update your production queue to include Drills and Suit Batteries.

If you’ve created a new Alter, build a Dormitory so they have a place to sleep.

With an empty research slot available, queue the Sheep Autopsy task to keep progress moving.

Head north through the cave behind the base and destroy the time dilation anomaly inside.

From there, mine a shallow Organics deposit nearby. You can also choose to move past it. At the top-right corner of the map—or by circling around—you’ll reach a high climb that requires the Hook Upgrade. If the research is finished, queue up its production immediately.

Cross the map, pass through an Energy Gate, and replace your battery with a fresh one.

Explore the forested area and the newly unlocked zone. On the right, you’ll find another Damaged Chip, but it’s surrounded by a large anomaly. Wait for the anomaly to shrink before destroying both cores. Then move in to retrieve the chip.

On the opposite side, locate a small Rapidium deposit. Ahead, you’ll encounter both an Energy Gate and a rock blockage—one on each side of the path.

The anomalies in this area are especially aggressive. Clear them out, then break through the rock.

This leads you to the main Rapidium deposit for the region. Be cautious when dropping down—it places you directly into a time dilation zone.

With the day nearly over, return to base and speak to the Doctor for any remaining updates.

Once everything is in order, end the day.

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Day 35 : Researching the Neutralizer Towers

Begin the day by manually crafting the Hook Upgrade at the Workshop, as Alters won’t begin their shifts until 9:00.

Once that’s done, head to the Dormitory to interrupt and resolve an argument between the Miner and the Technician.

Initiate research on the Filters, which will trigger the optional task “Panic Precautions.” Then check your resources and continue harvesting Metals and Organics to stay stocked for upcoming builds.

Next, set out toward the ledge climb where the Gravity Sensor must be placed. At the fork in the road, take the right path first to collect the items Body Swap and a Calendar.

Double back, take the left path, destroy a nearby Anomaly, and climb to the top ledge. You’ll find the Gravity Sensor location blocked by a pulsating anomaly. Wait for it to shrink, then destroy both cores and place the Gravity Sensor.

Around this time, the “Sheep Autopsy” from the task “The Value of Life” should complete.

Travel to the far northwest section of the map to retrieve the Class Photo and Watch.

Then cross the map toward the Energy Gate near the northern Minerals deposit. Break through the rock blockage, but be prepared for a Time Dilation Anomaly immediately afterward. If you lack the battery charge to destroy it, push through quickly.

After clearing the area, turn right and inspect the trees—you’ll discover they’re a hologram. Take the hologram back to base; this is important for progressing the Technician’s storyline.

Head to the climb near the northern Organics deposit. At the top, collect the Yerba Kit and Lucky Key Chain. This should complete most of the map’s collectible areas.

Set up a Travel Pylon on the northern side of the map to enable quick traversal and battery recharging.

From there, proceed to the Interal Vein and follow the path up to collect a Planetary Sample.

Return to base and speak with the Scientist. When prompted, choose “We should inform Earth.” Agree to upgrade the Infirmary when the option appears. Then ask about the Gravity Sensor, and take the opportunity to compliment the Scientist to maintain a positive relationship.

Bring up the filter issue as well. Once the conversations wrap up, new research options—“Filtering Jelly” and “Neutralizer Tower”—will be unlocked.

Speak with the Botanist about Lena, and give him the photo. Indulge his fantasy during the conversation—there’s no need to demotivate him.

Finally, speak with the Doctor and give him the watch. End the day by sleeping in the Infirmary to reduce your radiation levels.

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Day 36 : The Guard

Start the day in the Infirmary, where you’ve once again overslept. Since it’s already 10:00, immediately check your assignments.

To boost morale, focus on improving the quality of food in the Kitchen. Assign the Botanist and Doctor to kitchen duty to take advantage of their bonuses.

Next, head toward the high climb near the southern Minerals outpost. As you ascend the ledge, you’ll encounter an Anomaly right away. In the distance, you’ll spot what appears to be a Surface Exploration Vehicle.

Near the vehicle, pick up the movie “Mind Wipe.” Follow the path behind the vehicle to reach the southern Rapidium deposit, where you can build an outpost. If you don’t have any Pylons available, note the location and plan to return later.

Climb back down and head left. You’ll soon reach an Energy Gate. Pass through it and explore the area beyond.

Clear the rock blockage, then collect the items Marked Cards and a Book for the Alters. Mark this area on your map for future visits.

Once Base Expansion III research completes, return to base and speak with the Technician about the vehicle you saw earlier.

Proceed to upgrade the base to the next tier.

If you’ve completed the Qubit Chip, head to the Quantum Computer—this will unlock the final tier of research and allow you to bring in another Alter. Your choices will include a Guard or a Refiner. Choose based on your current needs; in this case, select the Guard.

(Though you may second-guess this decision later, continue with your current plan.)

Visit the Social Room and spend time with the Miner, who’s been underperforming. Play a game of Beer Pong with him to lift his spirits and help him return to full 9-hour work shifts.

Once morale is improved and all tasks are complete, end the day.

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Day 37: The 3rd Rapidium Ark

Start the day by heading to the Dormitory—you’ll receive a notification that the Guard has been born. Wake him up to get him active.

Next, check your resources and assign tasks across your stations. Be sure to optimize production and exploration roles.

Find the Miner and give him the Calendar. This triggers a short conversation about the air filters—complete it before moving on.

Your main objective now is to head toward the North Rapidium deposit. The southern deposit can’t be connected via Pylons, so it’s not viable for now.

As you reach the northern deposit, clear out any Anomalies in the area. Once the zone is secure, place the outpost and connect it back to the base with Pylons.

To save time, run south to retrieve the unused outpost you had placed earlier instead of crafting a new one.

With the reclaimed outpost, return to the North Rapidium zone, install it, and begin collecting needed resources.

Around 19:00, head back to base. You’ll receive a notification about a discovery in the Greenhouse—go there to find the Doctor.

You’ll discover they’ve uncovered a giant turnip. Wrap up the interaction, then take care of one last critical task: build the third Rapidium Ark for the objective “Three’s a Pattern.”

Once that’s complete, end the day.

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Day 38 : The Alters get MRI scans

Start the day by checking the kitchen—you’ll get a strange message about two food rations being stolen. Go there to investigate, but don’t expect to find anything unusual. Speak to the crew, though no one will mention the theft.

Next, give the Marked Cards to the Guard, then set up daily assignments and have everyone focus on resource extraction.

Once the MRI Module finishes crafting, install it in the Infirmary. Around the same time, Neutralizer Tower research should complete. Head to the Scientist and discuss it.

You’ll learn the towers require 160 Metals and 160 Minerals each. Since you’ll need two, make sure to add both to the production queue.

Begin research on Automatic Outposts if you haven’t already. While future research depends on your approach, it’s smart to start preparing for Act 3 now.

Use the rest of the day for exploration and mining—gather whatever resources you’re short on.

As evening approaches, return to base and head to the Infirmary for the MRI scan. This will trigger the creation of a Core Memory, prompting all Alters to gather in the room.

Finally, queue up Filtering Jelly in production, then end the day.

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Day 39 : As Good As a Feast

Wake up to a message: “Two Food Rations have disappeared from the kitchen.”

Speak to the Scientist first.

After your conversation, the Scientist will direct you to contact Lucas.

In the meantime, the Guard will want to talk—likely about the missing food. He’ll also request surveillance cameras.

Speak to all the Alters about the news from the Scientist. Morale will be low, so consider planning a movie night for later. For now, assign tasks and head out. Focus on producing the Filtering Jelly and the Surveillance Upgrade, then go mining.

Once the Filtering Jelly is ready, install it in the kitchen.

Next, head to the Comms Room and talk to Lucas.

Afterward, speak to the Doctor.

He will initiate the “As Good As a Feast” quest, which requires 3 raw food rations. Prepare that for tomorrow.

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Day 40 : The Surveillance Desk

Start the day by checking the notification: a magnetic storm is coming in two days—if you’ve already researched the necessary tech.

Notice if you’re nearing maximum storage. If so, build a medium storage unit.

Assign daily tasks, then head to the kitchen, where the Alters will be discussing the Filtering Jelly.

Speak to the Miner—he should seem noticeably calmer today.

You’ll receive a call for Lucas, regarding the Rapidium Ark. He’ll ask you to build more for the task “Every One Counts.”

Next, go out to mine minerals for the second Neutralizer Tower. While outside, expect a notification that the Surveillance Desk has been built.

Once you’ve gathered enough resources, construct the second Neutralizer Tower.

Continue collecting Rapidium until around 19:00, then return to base.
Install the surveillance system, then find the Doctor and hand over the 3 raw food rations.

To wrap up the day, go to the social room and watch a movie with the crew.

End your day there.

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Day 41 : Installing the Neutralizer Towers

Start the day by addressing a power failure in the kitchen—fix it immediately.

Once resolved, assign the day’s tasks, then head out to install the Neutralizer Towers.

Cross over to the other side to complete the installations.

After finishing, return to base and speak with the Doctor about the task “As Good As a Feast.” Unfortunately, you’ll find the kitchen is broken again.

Follow up with the Technician. Let him know that someone had tampered with the vehicle, and inform him you’re ready to move forward—though that won’t happen just yet, as most of the crew is sick.

Next, take the call from Maxwell.

You’ll now need to create a Tabula Rasa. When prompted, you’ll have to make a choice—stay neutral for now.

Afterward, talk to the Scientist about Maxwell’s proposal and choose to side with both the Scientist and Maxwell.

Before ending the day, speak with the Miner one last time.
Then, end your day.

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Day 42 : The Contemplation Room and the Feast

Prepare for the magnetic storm—it hits today. Stock up on Radiation Filters and Repair Kits in advance.

Although you’ll have the option to go out and harvest, choose to stay in and focus on side quests instead.

Start by speaking to the Technician—the conversation will be about the Miner.

This initiates the task “The Miner Needs Help”, which requires you to build a Contemplation Room. During this talk, also bring up Maxwell’s suggested cure. Even if you select “I am looking for another way,” the Technician won’t be pleased.

Next, speak to the Doctor and inform him that you’re searching for an alternative. Mention that you’re considering calling Lena.

Then, build the Contemplation Room and a Park with a Bench. This will progress the tasks “The Miner Needs Help” and “Green Refuge.”

Afterward, begin production of the Feast for the task “As Good as a Feast.”

Now, call Lena. Be cautious—you won’t be entirely transparent during this conversation.

After the call, the Botanist will share his opinion on the cure. Since you’ve already spoken with Lena, respond with: “You’re right, it’s unthinkable.”

Next, talk to the Guard, which will trigger the task “The Perfect Crime.” He’ll suspect the Technician.
Engage in a series of conversations with other Alters, until the Scientist suggests it might be the Guard himself.

Confront the Guard to gain the Lesson Learned: Shrewdness.

Assign the Miner to a Contemplation Pod as part of his therapy.

Wait out the magnetic storm while the Feast is being prepared. Once it’s ready, interact with the team to create a Core Memory.

End your night after that.

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Day 43 : The Magnetic Storm

Start the day under the ongoing magnetic storm, which still has 17 hours remaining.

You won’t be able to speak to the Miner or the Doctor—either due to a bug or because they’ll become available after the storm passes.

With limited options, head out and collect metal.

As you continue, you’ll notice you’re running low on Repair Kits. Prioritize their production immediately.

With little else to engage in during the storm, wait it out—stand by, monitor systems, and when you’re ready, end the day.

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Day 44 : The Tabula Rasa

Begin the day under pressure—the sun is closing in.

First, assign daily tasks, then go speak to Lena. You’ll have the option to tell her about the Alters or not.

She’ll launch into a rant about Maxwell, questioning his motives and raising concerns about what should be done with the Alters. Despite her warnings, choose to proceed with the Tabula Rasa approach.

Next, check in on the Miner, who is having a breakdown. You’ll find the Scientist already there, trying to console him.

Initiate the Tabula Rasa alteration via the Quantum Computer.

Then, talk to the Scientist—he’ll request time to finish his personal research, starting the task “Focus Time.” To support this, pause all research for 24 hours. Queue it up as soon as a research slot is free.

After that, speak to the Doctor about the Feast, then have a follow-up conversation with the Miner.

Once that’s done, head out to locate the new Interal Veins.
Use your map to pinpoint the first location—you’ll find the core positioned nearby.

The next Interal Vein is on a separate section of the map. Reaching it will be difficult—clear numerous Anomalies to follow the trail. Eventually, you’ll arrive at the site.

Return to base and find the Technician sitting in the park. Speak to him to trigger a Core Memory.

Finally, end your day and sleep in the infirmary.

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Day 45 : Blast from the Past

Begin Day 45 by checking your resource levels.

Wake up the Tabula Rasa—you’ll find the Scientist already waiting for you.

You now have three days remaining. Decide against making the implants if you’re uncomfortable handing control over to the Corporation. However, you can still craft the implants out of curiosity—nothing will happen if you’ve chosen the Tabula Rasa/Maxwell path.

Spend the day gathering minerals.

To improve morale, convert the dormitory into Personal Quarters for the Alters.

While exploring, you’ll discover another Interal Vein—but note that you’ll need to return tomorrow to address it.

Back at base, speak with the Botanist. Continue indulging his romantic memories of his wife until he mentions an axe Lena gave him. This will trigger the task “Blast from the Past.”

Next, talk to the Scientist. The conversation will eventually lead you to ask Lena about the axe—but since the day’s already been long, wrap things up and turn in for the night.

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Day 46 : Lessons Learned “Vulnerability”

Start the day by checking in with the Miner.

Assign him to the Contemplation Room for additional therapy.

Next, head out to locate the Interal Core. You’ll find it on the map near the South Mineral Outpost.

After retrieving it, return to base and speak with Lena. When you ask about the axe, she’ll say she’ll call you back later.

Follow up with the Miner regarding his therapy session. This will unlock Lessons Learned: Vulnerability.

While doing maintenance work around the base, expect a call from Lena at 18:30. She’ll send you a photo of the axe the Botanist had mentioned.

Update your production queue, then check on the implants—they should be complete. Speak with the Scientist about them.

To end the day on a lighter note, watch a movie with the crew to help lift their spirits.

Wrap up the day shortly after.

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Day 47 : Base Expansion Tier 4

Start the day with little on your schedule, so use the downtime to review your resource stockpile.

You’ll notice a shortage of minerals, prompting a trip to the North Minerals deposit to set up an automatic outpost.
Stock up on batteries beforehand—the area is filled with anomalies.

Clear all anomalies—there should be around five in the lowest area where the outpost will be placed.

Once the area is clear, set up the outpost and link the pylons to the nearby Rapidium outpost.

With your mineral supply restored, proceed to upgrade the base to Base Expansion Tier 4.

While the Scientist works on his personal research, shift your focus to developing your suit in preparation for Act 3.

Since your outposts are operational and base systems are stable, head out again and mine from shallow deposits scattered across the map until around 19:00.

Spend the rest of the evening watching a movie to wind down.

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Day 48 : Finishing up

Start the day by heading to the kitchen for a group meeting.

If you’ve already made your decision, proceed with the brain tissue treatment. Like me, you may choose not to trust the Corporation—but your path is up to you.

The Scientist will extract the brain matter, triggering a Core Memory—a small but meaningful win.
Be prepared: some Alters will turn against you no matter what path you take. In this case, the Technician, the Botanist, and the Doctor distanced themselves.

Next, speak with the Scientist about his ongoing research. He’ll offer a more efficient Radiation Filter blueprint.

Then, make the rounds and talk to each of the Alters individually.

Afterward, check your Organic resource count for the next phase.
If you haven’t already, now is the time to give the axe to the Botanist for the task “Blast from the Past.”
If you’ve completed the treatment already, he won’t accept it, so be sure to do it beforehand.

Now, gather as many resources as possible to prepare for your next step. Once you’ve collected enough Organics, assign four Alters to the Neutralizer Tower, then head toward the Gravity Sensor.

Unfortunately, upon arrival, you’ll find it’s outside of working hours, so you can’t proceed yet.

End the day and plan to head out first thing tomorrow.

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Journey 3 & Interlude

Day 50

Slowly wake up after the Technician’s attack. The Scientist will be there, waiting—he’ll inform you there are messages from Earth. Head straight to the comms room to listen to them. Also note: the angry Alters have absconded.

Afterward, speak to the Scientist. He will suggest that you should “upgrade” your mind.

Proceed to the Womb and step inside. This process will create another core memory.

You’ll wake up back at the base, disoriented but functional. Then, step outside.

Interlude

It all feels very Interstellar. Take a long jog through Jan’s psyche—you’ll move through fragments of thought and memory stitched together in a surreal sequence.

As for the dialogue choices along the way, don’t expect a major difference. Try either option; the responses will likely loop back to the same conclusion.

Once you wake up again, speak to the Scientist.

That’s when you’ll receive the Lesson Learned: Perspective.

After that, head over to Base Navigation and change the system.

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That completes the full walkthrough for Act 2 of The Alters.

Walkthroughs for the other Acts can be found here or below –