The Callisto Protocol: Aftermath Walkthrough (Chapter 3)

By Dave Acuñaon
The Callisto Protocol Chapter 3 Aftermath cover

Aftermath is the third chapter of The Callisto Protocol which follows Jacob’s escape attempt after being incarcerated in the Black Iron Prison for some unknown reason. Due to the outbreak that happened inside the prison, this gave Jacob the chance to break out of his cell, but this meant that he also had to make his way through the dangerous biophages that have taken over the facility.

In this guide, we will go through the events in Chapter 3: Aftermath of The Callisto Protocol, sharing tips and listing down any collectible that can be found in the chapter.

See previous Chapter 2 - Outbreak Walkthrough The Callisto Protocol

After surviving the fight against Capt. Ferris, with the help of Elias, Jacob finds himself navigating through the different sections of the infested Black Iron Prison, dealing not only with the biophages, but also with the security units that have activated their kill protocol.

Chapter 3: Aftermath Objectives

  • 3.1 Locate Elias in Security
  • 3.2 Print a weapon at the Reforge / Paper Jams Achievement / Reforged Achievement
  • 3.3 Exit Security
  • 3.4 Locate the medical facility
  • 3.5 Find a guard’s corpse / Data-Bios #5
  • 3.6 Open Laundry B202 door
  • 3.7 Locate the medical facility / Data-Bios #6 and #7
  • 3.8 Reach the back exit / Data-Bios #8 / In Striking Distance Achievement
  • 3.9 Look for an elevator / Data-Bios #9
  • 3.10 Find a way out of the basement / Workplace Hazard Achievement / Data-Bios #10
  • 3.11 Reunite with Elias
  • 3.12 Use gondola to reach the SHU / If the SHU fits… Achievement
  • 3.13 Restore Power / Data-Bios #11
  • 3.14 Locate the SHU control room
  • 3.15 Activate SHU controls
  • 3.16 Take elevator down to the cell
  • 3.17 Free the inmate / Data-Bios #12
  • 3.18 Reach the tram station
  • 3.19 Get through security / Terminated Achievement
  • 3.20 Exit the station
  • 3.21 Contact Elias
  • 3.22 Find the hatch

Locate Elias in Security

As you arrive at the next hall, continue moving forward until you see Warden Cole’s hologram. Continue down the stairs and prepare to be attacked by grunts upon opening the door behind the broken security unit.

Continue to the next room and squeeze through the door leading to the connecting access hall. You’ll then see a cutscene of incoming grunts, but Elias leads you to a side room.

Inside this room, search through the lockers on the left to get health and a bunch of credits, then go to the cabinet on the right to get its loot.

Follow Elias to the next room where he’ll hand you over a pistol and he’ll tell you to check the Reforge.

Print a weapon at the Reforge

Before heading over to the Reforge, check the crate on the right side to get items and enough credits to buy the BI-55 Pistol “Hand Cannon” for 800 credits. Purchasing the weapon will reward you with the Paper Jams achievement. After the following cutscene, visit the Reforge again and purchase an upgrade for any of your weapons to get the Reforged achievement.

Exit Security

Make your way out of Security and you’ll learn about the Strategic Targeting System that will help you take down enemies faster with your new firearm. Continue moving forward and you’ll see another grunt infecting and turning a guard. You’ll then have the opportunity to test out the new combat system on this enemy. After defeating it, continue towards the next hall.

Locate the medical facility

Continue through the hall until you find another grunt up ahead which you’ll have to perform a stealth kill on. Sneak up on it until you see the prompt to stab. Move up the stairs to encounter your first Big Mouth.

Big Mouths can shoot projectiles from their mouth which don’t deal much damage, but can stagger Jacob significantly and opening him up for an attack. Getting close to their melee range make them stop spitting, as well as shooting their heads off will do the trick; they can then be fought like a regular grunt.

After killing the Big Mouth, head towards the corridor to the left first. Explore the cells along it to get some more ammo and then slip through the hole in the window. Inside, you’ll find a ladder that leads downwards.

Down this lower level, there are grunts at the end of the path on the left, so head towards the path to the right first towards the crate. Prepare for a fight as opening the crate will lure the grunts to your position. Once you clear both of them, retrace your steps back to the hall where you fought the Big Mouth.

Now head towards the recreation hall where the Big Mouth came from to proceed. To the left is a huge window for Ward 03. You can hit it with a melee attack to break it and get some more loot inside. Go back into the main path and go round the path to the left to find an office with a bloody vent. The vent will lead you to a hall with a damaged security unit next to a guard’s corpse. Take note of this body for now.

To the left are two shambling grunts and the game will tell you to move quietly around them. Alternatively, you can sneak up on them for a stealth kill. Afterwards, approach the door to the Laundry Room that you won’t be allowed access to. Elias will then tell you to find a guard’s body to get credentials from it.

Find a guard’s corpse / Data-Bios #5

Go back to the guard’s corpse near the security unit and harvest its implant. You’ll then obtain Data-Bios #5: Sgt. Eric Jane: Locked Door.

Open Laundry B202 door

Head back to the laundry door and use the implant to unlock it.

Locate the medical facility / Data-Bios #6 and #7

Continue moving through the laundry room until you are at the place where you see the conveyor rails to the right. Prepare for a fight as one of the corpse lying on the ground is actually a grunt that will spring up as you approach it. After clearing it, move further ahead and you’ll have two doors to go through on either side. Head towards the door on the right first.

Move down the ramp and follow the path until you see a small opening you can crawl in. This will lead to an office where there are two glass panels that you can break to get some ammo and some credits. As you exit, you’ll see a washing machine that can be interacted with; you don’t have to open it as it has a parasite inside.

Continue down the path to the left and you’ll find another office with more ammo, credits, health gel, and a pristine energy converter inside. There’s also another corpse that you can harvest the implant off to get the Data-Bios #6: Ofc. Pruitt Matos: Laundry.

Retrace your steps back to the other door that we haven’t checked and go through it. To the left, is the door to Maintenance B414. We’ll get back to this door for now and let’s head straight. Open the panel to the right to open a door that leads to a room. To the corner of this room is a pristine energy converter that you can pick up.

Go to the vent to the right and crawl through it. Continue moving through the path downwards until you see a hole in the ground where you can jump down to. Move past the broken elevator shaft towards the blue lit door. Squeeze through the door to arrive in some secret room.

You’ll find the Data-Bios #7: Duncan Cole: Secret Room 1 on top of the table on the far end of the room. Before exiting the room, check the crate on the side to get some loot.

Head back out and take the ladder up the broken elevator shaft from before to get back up to the room we’ve been to. Prepare to fight two grunts as you exit the room; you can take the vent on the right side to get a possible stealth kill on one of them.

Go back to the door leading to Maintenance B414 to proceed. As you move along the path, prepare to et ambushed by a grunt that will bust out of the glass on the left. After killing it, continue moving until you reach the door tot he medical ward.

Reach the back exit / Data-Bios #8

As you move through the medical ward, you’ll see a doctor’s corpse on the ground. Harvest its implant to get the Data-Bios #8: Dr. Ewan Hayes: MedLab Outbreak. Up ahead is another crate that you can loot.

Follow the path ahead to arrive at a half open door that you can squeeze through. Inside, Jacob will find a GRP or the gravity glove which is another addition to his weapon arsenal. On the panel next to the door, grab the gate fuse which will be used earlier. Doing so will make more grunts appear in the later end of the room, so you can take it now or grab it later.

Move further ahead in the room and you’ll see a hologram of the events that happened in the ward.

Continue up ahead and you’ll encounter another grunt. Right after you finish it, a heavier grunt will land down from the vent above. This one will take more hits before it falls down, so take your time and try to block between those hits and you should eventually kill it. Depending on whether or not you got the fuse earlier, another grunt will appear which you can grab with your GRP and throw at the heavy grunt.

After killing all, don’t forget to stomp them down to get a GRP battery for your GRP. You can also try getting the In Striking Distance Achievement by using the GRP to lure in an enemy and killing it with a single melee blow. It’s best to do this if the enemy is relatively weakened to ensure that the melee attack will kill it, or try this later once you have gotten some upgrades on your Stun Baton damage.

Use the fuse to open the door into the Med Office. Then, head to the Med Lounge first to find more items to loot, as well as a Reforge where you can print upgrades for your weapons. Be careful about opening the lockers in the Reforge room as one of them has a parasite inside.

Exit the room and head to the Med Observation room to the left and then open the door at the far end to proceed.

Look for an elevator / Data-Bios #9

As you open the door, you’ll be in a room full of hanged and mutilated soldiers. One corpse on the ground has an implant that can be taken to get the Data-Bios #9: Ofc. Dachs Symmons: Hanged Guard. Proceed to the path on the left and squeeze through the door to the elevator shaft where a cutscene will play.

After surviving the elevator fall, Jacob turns around and walks towards the next area, but he immediately gets grabbed by a Bloodworm. These enemies can shoot their heads using their tentacle-like necks and latch on to its victims. Once it latches on to you, mash the button prompt to kill it and set yourself free. Alternatively, spotting one in advance will be helpful as you can pre-emptively shoot it to kill it.

Find a way out of the basement / Data-Bios #10

Move further ahead and prepare to be ambushed by a grunt from the left. You’ll need a gate fuse for the gate on the right, so head to the left first and climb up the ledge. Before moving forward, spot ahead to see a Bloodworm sac. Shoot it then proceed. Jump down the next area and prepare for another grunt from the vent below.

Continue moving ahead and you’ll see a huge fan with a Bloodworm sac near it. Shoot the sac then follow the path to the right to reach the back of the fan. Prepare for another fight as you’ll be facing against a heavy grunt. You can use the fan to kill it by using your GRP to throw the heavy backwards and into the fan. Doing so will get you the Workplace Hazard Achievement. Also, check the body nearby to get the Data-Bios #10: Ofc. Kerry Brown.

Head up to the next ledge, but before proceeding to the other side, there will be a couple of Big Mouths and grunts roaming around. Cut their numbers first by grabbing one of them using the GRP and pushing them on to one of the wall spikes. There are also other types of environmental damage that you can play around in this area.

Once the area is cleared, go to the locked gate next to the beheaded guard to find the gate fuse. Before using it to open the gate nearby, head back to the first part of this area where there was another gate that needed a fuse. Behind this gate is a vent that leads to a small room where you can find the schematics for the Skunk Gun.

Take the gate fuse again and retrace your steps back to the other gate to proceed to the next lift.

Reunite with Elias

Take the lift up to the SHU and follow the walkways until you reach the SHU Command 0701 where Elias is.

Use gondola to reach the SHU

After the dialogue, follow the path on the opposite side of the command room until you reach the bottom section that connects to the SHU. You will also get the If the SHU fits… Achievement for doing so. Down here, you’ll find another Reforge station that you can use. Ride the gondola to reach the SHU to proceed.

As you approach the SHU, prepare to defeat the enemies that are waiting by the gate. You can use your GRP to grab them and then release them to fall down the pit.

Restore Power / Data-Bios #11

Inside the SHU, go to the back and grab the two fuses from their panels. Pay attention to the med cabinets in case you need health; stock up as you’ll need it pretty soon. Head back to the gate and climb the crates to the left. Check the corpse up ahead first to get the Data-Bios #11: Tadgh Song. Afterwards, put the two gate fuses in the terminals and prepare for a fight.

Once the SHU is powered up, enemies will start pouring in in the area. Pay attention to the sounds as there will be an enemy crawling through the vents to try and get behind you. Use the GRP to throw the enemies towards the spike rollers while keeping them at bay by staying on the top level. Try to save your GRP charges to quickly deal with the heavy grunts first.

Locate the SHU control room

Once the enemies have been dealt with, proceed to the door between the two panels before. Eliminate the crawling heavy just behind the door, then climb up the spiral staircase to the next area.

Activate SHU controls

Before activating the controls at the panel, check the backside of the room first to get an energy converter which you can sell at the nearby Reforge station. Once you’re done with the upgrades, interact with the panel to proceed.

Take elevator down to the cell

Head back down the stairs and turn right to find the elevator. Take it to go down and prepare to fight a Big Mouth and some grunts that will appear later on.

Free the inmate / Data-Bios #12

After dealing with the enemies, you then have to find the inmate from one of the cells and free them. Access the panel on the right side to open up the cell. A cutscene will play and Dani will show up to lock Jacob inside her cell instead. After a short dialogue, you can then grab the Data-Bios #12: Dani Nakamura on the table. After the cell stops moving, open the panel and cut the wires to open the cell gate.

Reach the tram station

Once you step out of the cell, another grunt will be close by. Defeat it then proceed forward through the pipes. Once you reach the pipe where you have to vault over, there will be two sacs on the other side. There’s actually a third sac below the vent where the Bloodworm will show up, so prepare to be grabbed.

Pas the Bloodworm, crawl through the narrow space and you’ll arrive at another area covered in flesh and sacs. None of these sacs are active, but a bunch of parasites will be jumping at you. Clear them out, then look down the stairs from afar first where you’ll find a Bloodworm sac that you can shoot.

Go to the next area and crawl through the narrow space again until you find a ladder that you can climb down from. Once you’re down, prepare to be ambushed by a grunt popping out from the vent. Then, use the GRP to remove the vent cover. There will be a grunt at by the vent exit which you can eliminate.

Get through security

You’ll have to sneak past the security unit patrolling the area, or you can take it down which will get you the Terminated Achievement. Go through the path lined up with crates first while trying to avoid detection and gathering the ammo and loot along the way.

Once you arrive at a more open area, use the crates as cover and wait for it to get to a far enough position where you can still aim at its head. Depending on how upgraded your gun is, you can defeat the security unit within 3 to 6 head shots. Don’t forget to stomp them as they can also drop items.

Continue up ahead to the next area, but be prepared to fight the grunt that will show up before the vent.

Exit the station

You’ll have to squeeze through another narrow gap once more before you arrive at what is basically a trap room. There are moving spike rollers in the middle of the room that you must avoid by getting in between the safe areas near the walls. To make things worse, enemies will also be coming out while you try to traverse the trap. Before taking on the trap, check out the vent cover on the other side of the room and use your GRP to remove it. Inside the vent are some crates that contain some more loot.

Take advantage of the spike rollers to lure in the enemies to it before hiding behind the safe spots. It’s best to be blocking all the attacks and let the rollers do the job for you. The roller will only move if it detects something on the rail, so in order to clear your path, peek quickly to make the rollers move, then run straight to the next vent.

Contact Elias

As you reach the next safe room, Elias will contact you about the next plan.

Find the hatch

After your conversation with Elias, go to the back of the room and check the lockers first. Then, open the hatch through the panel and climb down using the ladder to complete the chapter.

Chapter 3: Aftermath Achievements

Here are the achievements that can be obtained in chapter 3:

  • Paper Jams: Print a weapon for the first time.
  • Reforged: Print a weapon upgrade.
  • Workplace Hazard: Use GRP to kill an enemy by throwing them into an environmental hazard.
  • If the SHU fits…: Activate the SHU.
  • Terminated: Take down a security robot.
See next The Callisto Protocol: Habitat Walkthrough (Chapter 4)

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Check out this video by theRadBrad showing the gameplay for Chapter 3 – Aftermath: