No known secrets.

Right after picking up the Shotgun, you'll enter a cave with railroad tracks. To the right there's a ledge with two Grenades on it. From that ledge, jump onto a flat cliff platform in the center of the room, and then onto a railcar sticking out of the tunnel. Crouch and climb into the tunnel for Cells and Adrenaline.
 
As you pass the red force field with a Tank behind it, you'll notice a Megahealth pickup on top of stacked crates. Collecting it gives you an encouraging message.
 
After you pick up the Railgun and get ambushed. One of the hexagonal hatches on the right of the bridge is open. Get inside, walk through the tunnel, then look right and do a 180 to get into an adjacent tunnel with Adrenaline in it.
 
Entering the gate after the bridge, you'll find a red security door. On the opposite corner of that door is a gate that is slightly ajar, with Combat Armor visible inside. You'll need to lob a grenade through the gate such that it lands into the open hatch and explodes there, then the gate will open fully.
 
In the room with two conveyor belts, in a corner between said belts there's a button on the wall. Shooting it will unlock a passage to a secret level: The Casali Effect. To get inside, either grenade jump or jump over other crates, starting with the small one in the back of the room.
 

No secrets.

To the sides of the red forcefield are two buttons. Pressing one will lower the forcefield, while pressing both - in any order - will spawn Combat Armor and count as a secret.
 
In the meat area with the Blue Key, mercy killing the insane marine will open up the nearby blast door and reveal two Brains enemies, which count toward the kill total.
 

No known secrets.

From the corridor with windows, follow the white line on the floor into one of the side rooms. Hidden between a couple crates is a crawlspace to a secret room with Adrenaline.
 
In this room, shoot the area around the writing on the wall with any explosive weapon. This will open up another door, unleashing a Shambler and revealing Cells and Megahealth.
 
As you collect the Blue Key, the doors on the lower level will open, releasing a swarm of Technicians. In the small room at the foot of the stairs, across from the "it's stuck" door, is another crawlspace, containing Slugs, Cells and Rockets.
 
After passing the blue security gate, shoot the black and yellow striped segment on the left hand wall. This will open up the previously stuck door across from it and allow you to collect Body Armor.
 
Falling through a wide vertical shaft, you will encounter four shootable switches around its perimeter. Shooting two of them will open up the floor and let you progress, but shooting all four wiill make an Invulnerability power-up spawn in.
 
This can still be done after falling to the lowest level.
 

No known secrets.

After first jumping into water, swim forward and into a pipe entrance. Halfway through the pipe, there's an intersection with another pipe leading upward. Follow it up and forward again for a Submachinegun.
 
You can still reach this secret after draining the water, if you shoot the grate and enter the pipe from above.
 
In the area where you need to use two alternating piston platforms to get out of the water, while riding the second platform, halfway up there's a ledge with Combat Armor on it.
 
While crossing a bridge you raised by stepping on a floor button, you may notice a dead marine on the cliff below and to the left. Jump down there and crawl under the walkway for an Adrenaline pickup.
 
In the area with blue lasers, drop down behind the pipes leading into water to reach a ladder that leads to Combat Armor. This can be done before or after draining the water.
 

Right at the start of the level, under the water is a cracked wall with an Invulnerability power-up behind it.
 
In a semi-flooded outdoor area adjacent to the big hall you can notice a rectangular opening in the wall with a dead marine in it. Drop down onto that ledge and loop around to reach a Bandolier.
 
After collecting the data disc, in the area where you find the Railgun and get ambushed by three Gladiators. There's another dead marine on a cliff ledge at the farthest wall. Navigate that ledge to find a hatch that leads you to Body Armor.
 
In the area on an upper level where three wall sections open up behind you, revealing enemies. Jump onto the farthest section and shoot a switch in the ceiling, then climb up to get Slugs and a Megahealth.
 
This one can only be accessed after disabling the blue lasers in Comms Bunker. In the outdoor area where the level starts and ends, take the lift to the highest level, then jump down to the ledge on the left, leading to an area from which a Gladiator previously spawned. Proceed through the opening previously blocked by lasers for a developer easter egg.

At the very start of the level, from the Railgun, look down and back towards the entrance for a balcony with a dead marine on it. Carefully drop down onto it for Quad Damage.
 
In the room with the big cargo lift, on the lower level, there's a dead marine and an Adrenaline pack on a ledge. Ride the small lift up, then drop down and collect it.

This episode is somewhat weird in the sense that you'll be mostly going back and forth between several sprawling levels. Instead of listing each level with all of its secrets, I will list the secrets in the order you encounter them.

Once you reach an open space, make a jump onto the slope to the left and continue forward for an amazing reward of a single Armor Shard.
 
In the next room after finding the Shotgun, there's an Adrenaline pack in one of the tubes. You can either jump over the wooden boxes and crawl inside, or enter an adjacent tube and loop back around to get it.
 

From the start of the level, go forward and into open air, until you reach a dark cave in the cliff to the right. Enter it, look up and shoot the planks over the ceiling to reveal a Chainfist.
 
In the same cave, go left from the entrance to reach a Bandolier.
 

After swimming through the pipes, you'll come upon a long room with wooden flooring. Halfway through the room, turn left and drop down into the half-pipe for Adrenaline.
 
In the open area with two waterwheels, after getting on top of one of them, make a slope jump upward onto the chute and climb to the top for Adrenaline.
 
In the same area, after flipping the second lever, jump onto the waterwheel spokes, then onto its axle, then onto the planks stuck in the wheel, then on the top of the newly opened hatch, then up into a secret room with Megahealth. 
You can also come back here later in the campaign when the drills have been retracted. A dark crawlspace in the back of the room will be accessible, leading to a Dopefish cameo and a shortcut back to the start of the level, though none of this counts as a secret.
 
After the waterwheels room, you'll come upon a room with slanted floor with a half-pipe running through it. Jump onto the wooden boxes by the left wall and proceed into the pipe for Double Damage.
 
In the spacious room with a big strogg ambush. Jump onto the crates in the back to reach Body Armor in a dark corner.
 
In the same room, dive into the water and swim to the end of the pipe for Adrenaline.
 

On the T-intersection where the front path leads to the Railgun and the left path leads to drill #2, turn right and drop behind the boxes, then navigate a long air duct for Megahealth. Alternatively, you can climb over the boxes from below.
 
As you emerge from the air duct from the previous secret, go forward until you see a door with a red lighting symbol, to your right. It's on the lower level, below drill #6 and next to a ladder and a slanted walkway connecting the floors. Shooting this door will open a secret room with a Hyperblaster, two Cells and a First Aid Kit.
 
After disabling drill #3, jump onto the terminal, then onto the drill housing, and climb around the drill. Behind it is a ladder that, through a series of air ducts and catwalks, ultimately leads to a Dualfire powerup.
 
After shutting down all drills, a room with lots of crates will open on the lower level, under drill #1. Climb the crates for Adrenaline.
 
After leaving the ship, in a room with the Grenade Launcher, there's a breakable wall towards the back, next to a Mutant corpse. Behind it, there's an Adrenaline pack, a bunch of Armor Shards and Stimpacks, and an entrance to a secret level: Pumping Station III.
 

No known secrets.
 

From the entrance, pass through the long corridor leading to the Double Damage power-up. The next room has a wooden crate in the corner with one of its panels broken off, leading to a dark secret area with Adrenaline.
 
Again from the entrance, look outside from the leftmost opening in the corridor overlooking a body of water. You can make a series of jumps from there to get a Plasma Beam. Watch out for a pitfall inside the dark pipe.
 
From the previous secret, get back out of the pipe and turn left. This is the area where the original entrance to Strogg Mining Intake was. The passageway previously blocked by the drill is now accessible, leading to a secret passage with Stimpacks, Bullets and Adrenaline.
 
In the same area, stand at the borehole left by the drill. Looking towards the stairs, jump into the hole and swim forward. You will reach a secret passageway with several pickups, most notably an Invulnerability power-up.
 
The room after the Rocket Launcher room has an explosive box tucked in the left corner. Blowing it up reveals a dark sewer passage with Adrenaline and Slugs.
  

In the area where you fight the Megatank, climb over the pile of crates at the right hand wall, then jump over to the next pile for a Megahealth.
 

In the hall with the Rocket Launcher, there's a shootable switch hidden behind the boxes opposite the stairs. Shooting it opens up an alcove to the right, with Quad Damage, Adrenaline and a Backpack.
 
In the section where you jump over containers floating in green sludge, as you reach an open space and a rock wall, turn right and jump towards a gate that is slightly ajar. It will open, revealing Adrenaline, Combat Armor and a Grenade Launcher.
 
In an outdoor area with a bridge over green sludge. Shoot the hanging container on the left, then climb on top of it and jump onto the gate in the wall, which will open and reveal a Super Shotgun with Shells.
 

In the room where monsters drop from the ceiling, the gate to the right of the corridor labeled "Installation" will open when approached, granting a Super Shotgun.
 
After entering the gate labeled "Launch Systems", you'll reach a large hall with two Strogg banners and a stairway. Underneath the stairway you can see a glowing button. On the pillar to the left there's a switch that retracts a part of the wall, allowing you to get under the stairs and reach this button, which opens up a passage to a secret level: McGee Station.
 
In a small intersection room with a terminal in the center and a yellow forcefield labeled "Launch Systems" to the side. The terminal is cracked and can be destroyed, revealing a Double Damage powerup.
 

After collecting the Blue Key, return to the room with conveyor belts. The blast doors around the room will open, releasing enemies. Behind the rightmost blast door, which is directly opposite the Blue Key room, there's a red-and-black striped section on the wall. Shoot it to reveal a secret passage.
 
Within the secret #1 area, build up some speed around the U-pipe to reach the Dualfire powerup in the back.
 

Once you reach a round room with a ladder in the middle. Jump in the water opposite to the entrance, dive and turn around. At the bottom of the pool, in the center, there's a Railgun with Slugs.
 
After you drop down from inside a rusted pipe and land in a blue-lit pond. Climb the mountain of junk, turn around and make a running jump into the hole in the pipe for Adrenaline, a bunch of Stimpacks and an optional shortcut back to the start of the level.
 
In the tall multi-level room lit by an orange glow. On the top floor, check the dark area behind the boxes for Body Armor.

In the compound, in the tower with the Railgun there's a cracked vent that leads to a Megahealth.
 
To the right of said tower, after passing under a bridge, loop around and back up onto the bridge and open the door for Double Damage and a shortcut back to the level start.
 
As you move around the perimeter of the compound, just before entering the facility labeled "Control", turn around and make a jump into a dark passage hidden in the wall between two Strogg insignias, where you'll find a dog photo.
 

In room with a vertical stream of sludge in the center, where you fight an Arachnid. After disabling the lasers and climbing up a ladder, look for a button under the ceiling, over the pathway through which you originally entered. Climb over the air duct and shoot the button to access a secret level: Baklava.
 
This one is accessible after making a detour through Surface Infiltration to disable red lasers. After cutting off the flow of sludge, make your way back down into the Arachnid room and enter the drain where the sludge was previously flowing off to for a Plasma Beam.
 

Directly underneath the entrance to the level, under the bridge over the molten metal is a platform with Adrenaline.
 
Similarly, under the farthest bridge from the entrance is a platform with Megahealth.
 

After disabling the mainframe and climbing out if, turn around and check the base of the mainframe for the Disruptor.
 
After disabling the mainframe and making your way out of the shaft, right as you exit the mainframe area you'll come upon a doorway previously blocked by lasers. It leads to a room with three electrical jumpers on the wall. Shoot them to reveal a Quad Damage powerup.
 
After the mainframe is disabled and the lasers switched off, make your way back to the start of the level, where you crawled out of an air duct and found a Hyperblaster. The door in the far back will now be unlocked. Enter the room to reveal an Adrenaline pack and a secret bossfight.
 

Right before the second laser gate, after you break an air duct cover and climb inside, you'll find yourself in a tall room with an elevator. Ride the elevator, drop down onto the square rock platform in the center of the room, then onto a stack of boxes. Break the grate covering for an Invulnerability power-up.
 
In the final room, where you fight the Overburden supertank. In the lava lake, towards the rightmost corner there's a shootable switch that opens up a room with cat pictures and some ammo. Entering it will make the usual message about finding a secret pop up, but it doesn't actually count towards the total.
 

In the hall with a Hyperblaster. After defeating all enemies, a stone lift platform will descend. Ride it to the very top and turn around to find a shootable switch that leads to a secret level: Turbine.
 
In a large cave where you get the objective to "Gain access to lower chambers". Going around the area, you'll pass through a room with brick platforms jutting from the lava. Below them, in the lava is a Megahealth pickup.
 
In the room with a huge piston riding up and down the shaft. Get on top of it, wait for it to get to the top, then turn to the left and drop down onto a platform with Combat Armor.
 

No known secrets.

No known secrets.

As you enter the 3x3 hall where the main battle takes place, look up. The skylight in the section directly to the right of the entrance is covered by planks that can be shot to make an Adrenaline pack drop down. 
 
Similarly, the farthest skylight from the entrance also has planks over it and can be shot for a Double Damage power-up. 
 
 
Call of the Machine was only released several days ago at the time of writing this guide, and I only searched for the secrets by myself, meaning there's a good chance I missed something. If you find anything else of interest, leave a comment and I'll add it to the guide and properly credit you.

─ 2023.08.18 update ─
Fixed some errors, added an easter egg, reformatted and reorganized the guide. Thanks to:

• erc for pointing out my mistake in the Mainframe section and for showing off the easter egg in Security Annex in their own guide, which was published practically at the same time as I did mine!
  
• Xazuki for showing me a couple formatting tricks in their own guide, which is beautifully presented and illustrated!

If you found my guide useful, consider buying me a can of coke on donatty[donatty.com]
or boosty[boosty.to]

Thank you for reading!