This level contains only a single (unmarked) secret.
As per Quake fashion, Dimension of the Machine has a start map of its own where you select the difficulty level you like to play on by going through the appropriate portal. Likewise, the highest difficulty level, Nightmare, can only be reached via an out of sight one.
To access Nightmare difficulty, go towards the portal that leads to Hard but instead of stepping into that one, jump into the opening to its right and follow the passage till you come across the related portal.
This guide assumes you are opting for Hard or Nightmare. On lower difficulty levels, items found by discovering secrets or the encounters mentioned in the descriptions may differ.

This level does not contain any secrets.
As the map name suggests, The Machine serves as the hub with five open portals that lead to the five distinct realms found within the dimension, with a sixth one becoming available only after you collect five runes from the said realms. From the starting point, the chamber to your left has three portals that lead to the realms of Machinists, Blacksmiths and Stonemasons; while the one to your right houses the two remaining portals to the realms of Cultists and Astrologers. You can tackle the realms in any order, but since the map / file names suggest so, the guide follows (and recommends) the order outlined above.

This episode consists of three levels that contain a total of 15 secrets.
---
MGE1M1: THE PAIN DRAIN
1/5 - As you enter the facility, jump on to the railing to your left and look down to see a biosuit. Jump down, get the suit and continue by the slime to reach a power-up.
2/5 - On the same spot with the previous secret, push the button next to the power-up. Move on and exit the slime pit. The door opposite the gold key door should now be open. Get in there and explore.
3/5 - In the room holding the silver key, look up by the door with an armor behind it and shoot the button open up the door in question. While you are here, hit the two identical rune plates found within the area. Find two more of the same plate in the next area that houses the gold key and hit them too. After hitting all four of them, an on-screen message states that 'a door has been opened'. Keep going on your merry way, for now.
4/5 - In the room accessed by using the gold key, an armor can be seen residing on top of a beam. Simply jump your way to it with the help of the nearer beam. You need to make a 180 degree turn in the air during your second jump.
IMPORTANT: If you want to get 100% kills for the level, follow the path before you and kill the remaining monsters that are located more or less around the next corner; but do not go through the pipe beyond the bridge that acts as the exit, because the fifth and the final secret leads to a secret level.
5/5 - Return to the central elevator. Assuming you shot the four rune plates as described in the third secret, an alcove on the second floor with a biosuit and a floor button inside should now be open. Get the biosuit -stepping onto the button in doing so-, drop down to the lower floor and dive into the slime pit to find the newly-opened gate. Swim through it to access the secret level, Sandy's Room.
---
MGE1M3: SANDY'S ROOM
1/4 - In the first room, hit the bloody demon plate to reveal a hidden compartment.
2/4 - In the room that houses the silver key, shoot the bloody demon plate below the walkway to reveal another hidden compartment.
3/4 - While going through the rather large hall with the gold key door on one end and a locked one on the other, look for another bloody demon plate to hit that reveals yet another hidden compartment.
4/4 - Following on from the previous secret, drop down to the floor below as you cross the bridge surrounded by lava falls to find a hidden weapon and some ammo.
---
MGE1M2: THE WISHING WELL
1/6 - In the first room, go to far left and hit the grating on the wall to access the armor that resides behind it.
2/6 - In the room with the giant gear on one end and the gold key door on the other, look for another grating on the wall and hit it to get the ammo residing within.
3/6 - Following on from the previous secret, look for a button hidden behind the planks on the left and shoot it to open the door next to it that leads to a hidden area (albeit a nasty one).
4/6 - In the slime pit, look for a slightly out of sight floor button behind a grating. Step on the button and check the other side of the pit to find a megahealth that can now be picked up.
5/6 - Go to the very end of the room beyond the silver key door to find the stairs leading to the lower floor. Press the two buttons found on the consoles to open the next door that leads to a hidden area.
6/6 - As soon as you get the gold key, jump onto the pipes behind the pillar and get to the other side of the walkway to find a megahealth.

This episode consists of two levels that contain a total of 18 secrets.
---
MGE2M1: ACID SANCTUARY
1/10 - Right at the beginning, make your way to the area behind the portal to find hidden ammo.
2/10 - Upon reaching the bridge that leads to the main gate, look to your left to see a narrow ledge. Jump down there and turn the corner to find some ammo on the other side.
3/10 - Still on the bridge, this time look to the left of the main gate to see a semi-hidden portal glowing red in the corner. Utilize the bricks across from where you are standing and then the pillar next to it to make your way to it and get teleported to a ledge overlooking the gate that houses a quad damage (might be better to use it later though).
4/10 - On the second floor of the ruined building next to the bridge, use the jut of the pillar as a stepping stone to jump across and reach the armor on the other side.
5/10 - On the floor where you need to press a button to open the door to the adjacent building, look for a ledge at the back of the room that you can drop down to and continue towards the light to find a megahealth.
6/10 - Jump from the walkway to the roof of the sunken tower below and check inside the one next to it to find a grenade launcher and some ammo.
7/10 - Before getting the gold key, drop down into the opening on the roof you are on to find another hidden weapon.
8/10 - As you reach the top of the scaffolding on your path, move left alongside the ledge overlooking the pit and jump across to a thinner one that juts out from the rocks to find a hidden alcove with a megahealth inside.
9/10 - Before going into the the sunken tower, utilize the bricks next to it to reach the rocket launcher residing on the ledge.
10/10 - At the top of the sunken tower, before going into the intact one next to it, drop down to the lower floor to find an armor hidden away in the corner.
---
MGE2M2: FADING EMBERS
1/8 - Get the first elevator on your path moving by stepping onto it, step aside and drop down into the opening to get the items residing below.
2/8 - After getting teleported out of the previous secret, check the path that lies on the other side of the elevator to find an otherwise out of reach armor.
3/8 - Before taking the stairs leading to the other side of the facility, drop down to the ledge below and follow the path to its end to find a hidden lightning gun and some ammo.
4/8 - Following on from the previous secret, turn around after passing through the tunnel in the middle of the walkway and jump to the ledge to get the lightning gun.
5/8 - Right after the previous secret, look for a button in the corner as soon as you drop down to the next area and shoot it to reveal a tunnel that leads to the armor seen residing on the ledge.
6/8 - Shortly after going through the gold key door, jump across to the ledge below the stairs and follow the path by the outer wall to reach a hidden armor.
7/8 - Next to the tower top, jump down from the walkway to the top of the tunnel below to get the ammo lying out in the open.
8/8 - Returning from the previous secret, get on the roof to the left of the tower and turn around to find a ledge with the part of the wall above it looking slightly indented. Jump onto the ledge and hit the wall to access a hidden room.

This episode consists of two levels that contain a total of 19 secrets.
---
MGE3M1: DOWN THE WASTE
1/11 - On the floor below the gold key door, hit the bloody blind to the right of the tunnel entrance to access a hidden room.
2/11 - Following on from the previous secret, once you get across the slime pit in the tunnels, turn left and shoot the button that can be seen at the far end behind the crates. Return to the other side of the pit and get the armor.
3/11 - While swimming through slime, look for an alternate path to your right and follow it to reach an otherwise inaccessible room.
4/11 - Once you reach the second floor of the building connected via an overpass, look for a bloody grating in the corner, shoot it and drop down to find another hidden room.
5/11 - Activate the crusher on your way by stepping in front of it, step back and jump into the area behind it to find a hidden cache.
6/11 - Right after opening the silver key door, jump on top of the crates directly in front of you and drop down to the other side to find a hidden area.
7/11 - Following on from the previous secret, look for a button behind the two crates to the right. Shoot it, quickly turn the corner, take the stairs, get on top of the crate and hit the two bloody blinds that stand in your way to finally reach an armor.
8/11 - Following on from the previous secret, check behind the crates on the right side while making your way across the lava-filled room to find a ring of shadows.
9/11 - In the same room with the gold key, jump on top of the singled-out crate in the slime pit and turn around to find a hidden armor.
10/11 - Right after picking up the gold key, jump into the opening to your right via the crate in front of it to pick up a quad damage that comes in handy for the final rush.
11/11 - Before leaving the level, get on top of the crate to your right and make your way around the room (by first reaching the ledge on the opposite side, then jumping onto the beam above the exit elevator and finally hopping onto the other ledge) to pick up the lightning gun residing above.
---
MGE3M2: HELL OR DARK WATER
1/8 - While battling it out in the initial area, look for a part of the wall that differs in texture pattern next to either one of the lift buttons and hit it to reveal a hidden tunnel ripe with ammo.
2/8 - Just a few corners before the silver key where a megahealth can be seen through the windows, dive into the water by way of an opening on the side and swim around to find a quad damage and a ring of shadows, as well as some ammo and a health pack.
3/8 - In the room where you pick up a rocket launcher and battle a group of vores, look for a hidden button near the ceiling at the very end of the area and shoot it to open up the door featuring a demon on the other end. Check the room to find an armor and some ammo. The button can also be shot by surfacing midway as you swim through a lengthy pipe, if you happen to take the other way around to reach the room in question.
4/8 - In the corridor that leads to the silver key door, dive into the water and resurface right next door to find a hidden cache.
5/8 - As soon as you open the silver key door, shoot either of the two buttons that can be seen through the openings on the sides and get in there. Turn the corner, hit the bloody panel in the middle and follow the vent behind it until you drop down to a side room housing a quad damage.
6/8 - Following on from the previous secret, hit the bloody demon plate midway through the hall of crushers to access an out of sight ledge with some ammo.
7/8 - As you get past the second ceiling crusher, hit the bloody demon plate in front of you without dropping down from the crates you are on and jump in to reach the armor residing on a lower ledge.
8/8 - While making your way through the platforms moving over lava, shoot the button located on the second pillar to reveal a compartment and jump inside. Turn around to find another button on the first pillar and shoot it to reveal a megahealth.

This episode consists of two levels that contain a total of 6 secrets.
---
MGE4M1: GRAVE MACHINE
1/3 - Upon entering the crypt, look for a wall panel with different texturing, hit it and jump into the opening to find an altar behind.
2/3 - A little way into the underground tunnels, turn around and shoot the button on the wall to open up a hidden compartment that contains an armor.
3/3 - Following on from the previous secret, dive into the water near one of the two buttons that you need to press for progression to find another armor and some ammo.
---
MGE4M2: A GRAVE MISTAKE
1/3 - In the slime-floored room, shoot the two buttons on both sides as well as the slightly hidden one above to reveal a hidden compartment.
2/3 - Following on from the previous secret, shoot the button on the ceiling of the next tunnel on your way to open up a hidden compartment that contains an armor.
3/3 - Moving through the inverted monastery, turn left before jumping on the run-down door and continue towards the perforator at the end. Shoot the stained glass and look down for a narrow ledge you can land on. Drop down there to find a quad damage and some ammo.

This episode consists of two levels that contain a total of 11 secrets.
---
MGE5M1: NAZARD TERMINAL
1/4 - Upon start, look to your right for a bloody demon plate and hit it to reveal a hidden nailgun.
2/4 - In the control room, press the button hidden behind the crates in the corner of the lower floor to open up a hidden compartment nearby.
3/4 - Beyond the gold key door, shoot the three buttons found in the vicinity to lower the force field that stands between you and a perforator. The first button is right above the field itself, the second one is above a door around the corner in the same room and the last one is between the consoles on the lower floor of the adjacent room.
4/4 - Before leaving the level, turn around and shoot the square panel next to the non-functional door to reach the adjacent room where an armor resides.
---
MGE5M2: TOO DEEP, TOO GREEDY
1/7 - As you go through the ruined tower at the beginning, turn right after crossing the plank and make your way around the ledge to the window on the left. Drop down to the other side to get the armor lying out in the open. It is also possible to reach the armor in question by dropping down through the window next to the nailgun on your path.
2/7 - Following on from the previous secret, take the upper path in the next area and make use of the ledges to the right to reach the upper floor of the tower. From there, jump into the ruin next to you to find a megahealth.
3/7 - When you reach the mine entrance, check the right corner to find an opening obscured by leaves. Follow the tunnel behind to find a rocket launcher.
4/7 - After clearing out the mess hall, look for a blinking button under the counter and press it to open up the nearby meat locker. Have a look inside to find a perforator and some ammo.
5/7 - Simply jump down and grab the armor on top of the crates while crossing the walkway you activate as you progress through the facility.
6/7 - As you go through the trap-filled lava pit, look for a total of six buttons within the area and shoot them in the process. Doing so makes a set of pillars raise from lava next to the gold key. Collect the items on offer and follow the path for a safer return to the gold key door.
7/7 - Right after the two hovering platforms, keep an eye out for an armor residing on a lower floor of the centrepiece. Drop down from the topmost point of the walkway you are on to the outer ledge surrounding the lower floor and get in through the window to reach it.
---
Easter Egg
Before leaving the level, ride the elevator in the room before the portal that takes you back to the start. Return to the mine entrance and climb on top of the ruined tower that bars the other gate in the area. Shoot the newly-revealed button that can be seen through the opening to open up a vent on the side. Take the vent and press the button within to meet an old friend once more.
Note that you need to find all of the secrets within the level before attempting this, otherwise the shootable button is not revealed at all.

This level contains only a single secret.
1/1 - Once you down Chthon for the first time, the area at the back of the lava pit becomes accessible. Explore the path between the crates to the left of the elevator that leads to the silver key to find the only secret within this level: a quad damage.
'Exalted warrior from the machine... You are the master now. We salute you.'
---
Other dimensions await...