To 100% a level is to kill all enemies, find all secrets, and beat it without dying. When you select a level, you can see at the bottom which you have done (cross-hair for kills, lock for secrets, skull for no deaths). You do not have to do all 3 in one run, but if you are playing on a lower difficulty, it is pretty straightforward to do so. You must complete the level to save these medals.
100% of kills on all maps is generally pretty easy. There are occasionally enemies inside of secret areas, so I suggest getting 100% of kills and secrets in the same run to be safe. You can check if there are enemies around you left with the minimap - they are marked with red cylinders.
Some of the secrets are missable by going too far into the mission - if you collect them in the order listed, you 'll be all set.
Below is a list of all the secrets on each map, in the order of the maps.
Sacrum
1/5 After you fall down into the area with the partially opened door and collect the nexus point, the next room has what looks like 3 beds or tables. The door next to them can be interacted with to reveal a secret.
2/5 At the red key elevator, climb on top and jump over the nearby glass wall.
3/5 Immediately after secret 2, head outside and jump on the rocks next to the left and then again into a small area with armor.
4/5 Right after collecting the Shredders, drop down and turn around. There is an intractable door here with a faint "interact" symbol on it. Open it to reveal a secret ore.
5/5 After collecting the red key, immediately go left to find a ramp. Follow to the end for secret.
Research
1/5 In the opening area, behind where the portal is, go around the fence and follow the path to find a secret.
2/5 In the opening area, to the right of the switch you need to press to progress is a box. Jump onto it, then onto the ledge next to it to find some secret armor.
3/5 In the room where you open the door containing Bloaters, look behind you and shoot a switch behind a mostly closed door.
4/5 Before entering the large door mentioned in the above secret, jump on the nearby yellow crate on the left and find a small vent containing a Crawler.
5/5 After picking up the yellow keycard, the next room will have 6 columns. Behind one is a switch that open a nearby door with a medkit. You must step on the medkit to get the secret.
Fuel
1/6 Right at the start, go to the other side of the train, and shoot the target to access a secret ore.
2/6 After clearing a brief interior section, you'll be back outside. You can go down a ramp on the right or a door on the left. Go down the ramp to the end and press a button for a secret.
3/6 At the end of the ramp with exploding barrels rolling down it, double jump up to where the fiend was for a secret
4/6 Before you jump up the crates to go through the vent shaft, turn around and activate the switch to find a secret rocket launcher.
5/6 In the room with the rune, standing on the rune and facing the nexus point, the moving pistons on the right side have a switch in the corner.
6/6 In the room with sludge on both sides that has pillars than come down and crush the enemies, on the right side behind 3 red struts is a secret ore.
Wretch
1/5 At the first nexus point, jump up the little ledges to the Automap
2/5 After activating the short bridge and crossing it, go into the next set of rooms. To the right of the door is a switch - push it to access a rune.
3/5 In the sewer agitator, there is a nook on the right side with a rune and a switch to the left. Press it.
4/5 You will come to a section where you have to jump across 2 rock pillars to continue - to the left is a cave with a secret armor pickup.
5/5 After you get the nexus point at the top of the waste facility tower, hop up on the cliffs in front of you and over onto the support beam for a secret.
Chaos Generator
1/4 After destroying the shield twice, jump onto the large pillar and to the right over to a secret automap.
2/4 In the last shield area, after destroying the void reaper, go to the very back and look to the left (while facing where the void reaper was) for a switch to shoot. Take the elevator and follow the path.
3/4 Before leaving the area with the void reaper, look up and to the right for a switch on the wall to shoot.
4/4 In this same area in front of the door, jump up on a pillar and shoot the satellite with a rocket. This will open a path behind you in the second shield area. Follow it to the end for the secret.
Trial: Shotgun
1/3 Before extending the bridge after the red energy gate, drop down underneath it using the two little holes at the start to a ledge and follow to the end.
2/3 Before jumping into the exit hole, hug the left and go down a few ledges to find a secret rocket ammo
3/3 To the left of the exit hole is a ramp. Follow it all the way up to the top of the level for another secret.
Genesis Part 1
1/4 After you see The Crater displayed, go around the corner. In stead of jumping up to the next platform, go under it to the right for a secret.
2/4 In the next room, a door opens and a zombie shoots you. Go down the path to the right to hit a switch, then go behind where the box moved from for a secret.
3/4 At the bottom of the crater, a wall to your right will crumble down revealing a nexus point. To the left is a lava pool - at the back of that pool is a secret.
4/4 In the next area, you will have to activate a switch to lower a gate to continue. To the right of this switch, there is a crack in the wall. Drop down to find a secret armor.
Genesis Part 2
1/5 Get to the bottom of the lava fall area in the beginning and turn around. Go left towards a metal dam, to the right of this is a small cave.
2/5 Upon reaching the fortress, there is a target on the top left and right of the wall, on both sides of the door. Shoot them.
3/5 In the very next area, there is a small rock bridge over the lava pool. There is a platform under it with 2 health pick ups. Go down there and look directly up for a switch.
4/5 After the slayer fight, go up the elevator and turn around. Jump on the rock pillars to the right to find a small hidden area.
5/5 Before exiting the level, jump on top of the train to access a secret armor in the back left.
Trial: Shredders
1/2 At the second grinder that crushes the enemies, quickly jump onto it after shooting the switch to raise it and grab the automap. You can also get this using double jump after the grinder goes up by going up the metal ramps to the side of it.
2/2 Jump down to a cave in the lava in the last area for a secret.
Excavation
1/7 Right at the start, jump out into the lava and go right to find a switch. The secret trigger is the Rune just to the right of the box.
2/7 Drop down to the right when facing the green key building to find a switch which activates the lifts. Ride them up, press the switch and grab the armor.
3/7 In the area with the gate, go left. On the opposite side of the 2 doors is a faint switch.
4/7 On the yellow key path, some armor is obscured by a yellow shield. Bank a grenade off the lights to the right to hit the switch.
5/7 After getting the yellow key, you'll go trough a set of double doors. Immediately on the right after this door is a wall you can activate. Ride up and walk onto the bridge for the secret.
6/7 After getting the yellow key, you'll go through a room with what looks like computer terminals. In the next room you'll go down a small elevator - jump across the the health pickups and follow the tunnel.
7/7 On the green key path, you'll go up some stairs with lava, then more after. Jump out into the lava area, turn around, and shoot a grenade over the wall to unlock a secret.
Memoriam
1/1 Jump onto the grates at the very back right of the stage and look down and to the right. There is a small ledge (you can see it on the auto-map). Shoot the red-ish area to reveal a secret
Marksman
1/5 Shortly after the green energy door on the left with the key behind it, after going through a small room, stay to the right of the ledge to find a small cave.
2/5 After dropping down the yellow hole, go around the cliff to the right.
3/5 After killing the marksman, shoot the target on the wall, then activate the switches to drop the yellow shields. In the area on the left, there is a small nook with a secret ore in it.
4/5 On the way back through the level, you'll come to a green door blocking your path. Turn around from it and jump onto the open yellow create, then up to the ledge and down the path to a minigun.
5/5 To the left of the next main green door is a vent shaft. Go through it for the last secret.
Descent
1/5 Immediately upon starting, there are rocks you can climb to the left up to an Automap.
2/5 After unplugging the first plug, double jump and dash over the the Ore in the vent hole and fall down, shoot the target.
3/5 After unplugging the second plug, go in the other door before dropping down. There is a small switch on the left side near the floor.
4/5 On the same floor, one of the pillars is activatable.Opposite side of the plug - just rotate around all the pillars spamming activate until one goes up.
5/5 Immediately from the 3rd plug switch, go right down a tunnel to the end.
Hazard
1/7 After coming across the rune-locked exit portal,go right around the large rock structure after the second pad to find a small alcove
2/7 Right after the green double door, on the left side near the floor is a tiny button. Jump down where it opens.
3/7 Behind the green key switch to open the two metal doors, there is a room with some metal crates. Top left corner has a ventilation shaft to enter.
4/7 After raising the toxic level with the green switch, jump across the toxic sludge to the right and open the chest.
5/7 Make your way left of the green switch. Under the structure where a sniper spawns is a target. Shoot a grenade through the hole high above it.
6/7 After raising the sludge a last time, go left from the switch. Go through a rock archway and all the way at the back on the left side is an alcove.
7/7 After lowering the sludge and coming back outside, look down and to the right. On one of the rock structures you can see a white switch. Jump to that and activate.
Trial: Rockets
1/2 Around halfway through, you'll drop down and there will be yellow shield doors on the left. Shoot the target down the hall to disable the shield and pickup the Automap to unlock the secret.
2/2 After you blow a hole in the rock wall, shoot the next target but do not go in the opening door. Go around to the right and jump down onto the rocket ammo, then drop down again for the last secret area.
Meltdown
1/8 Once in the main structure, take the lift directly to the right of the nexus point. At the top, there is a switch in between the two green 02 walls. Press it.
2/8 Drop back down and go through the door on the yellow key side. Immediately to the left is an activateable wall with a faint symbol on it. Enter for secret.
3/8 Just forward from secret 2, look to the left of the toxic sludge. Shoot the target to extend the bridge. Cross for secret.
4/8 Through the green key door, on the left is a building with a yellow shield. Jump up on the boxes to the right and drop through the roof.
5/8 After the elevator where you are ambushed, in the next room, jump on the boxes in front of you, then across to an ore and some pickups.
6/8 Drop down where the smelter buckets are coming up from to find a secret armor.
7/8 Go back to the elevator where you were ambushed, you can now drop down into a secret.
8/8 Drop down and go to the left in the toxic sludge near secret 7 to find an alcove with rocket ammo.
The Forge
1/6 Just before the first nexus point, press a button on the back of the nearby pillar and drop down the hole.
2/6 In the room with the first marksman zombie, on the right raised platform is a switch behind a small pillar. Enter the tunnel it opens for an Ore and a secret
3/6 After activating the rising platforms, ride up and turn around to find a tunnel leading to a secret armor.
4/6 In the next room after the lift, there is a button on the column in the middle which opens a secret behind it. Drop down.
5/6 After collecting the yellow key card, jump across the lava channel and push a yellow button near a lava pit. This will activate two sets of moving platforms. Ride them up to find an opening in the wall.
6/6 From the previous secret, jump off onto ledge surrounding the room where you found the key card to the right. Follow the ledge and push the button.
Corruption
1/6 In the starting area, jump up to the ledge on the right with the 3 health pickups, then the ledge behind it, then the pillar, then into the shaft with the armor pickups.
2/6 Back right corner of the starting area, double jump up to find a tunnel with rocket ammo.
3/6 In the second area, when you activate the train on the left, go behind where it spawned to find a small secret pocket.
4/6 In the second area, on the right side in the middle, there is a small vent with red lights on both sides (the train stops below it). Shoot a grenade in to unlock a secret.
5/6 To the right of a building with a generator switch + fenced off rune is two ramps. At the top right of the first ramp is a tunnel, at the end are explosive barrels. Shoot them to reveal a secret.
6/6 At the base of the building which you have to drop through a hole in the roof for a generator switch (in the middle of the area) is a partially broken grate. Shoot it and go inside to find a secret.
Trial: Grenade
1/4 Near the beginning, there is a target on the left side in the area with the 3 column/buckets you shoot the grenades into. In between the 2nd and 3rd target of that area.
2/4 After the second elevator, there will be a ramp with a switch above it. Shooting the switch opens and area underneath the ramp, enter it to unlock a secret.
3/4 Before the SMG switch, go up the stairs to the left. There is a series of 3 targets to shoot which will unlock a secret.
4/4 After the SMG switch, only shoot the next target a little. Drop down to the right and there will be 3 switches to shoot, revealing a secret ore.
Atonement
1/4 At the very back of the main chamber, past the nexus point, in the tower with the Triforce on it, at the back is a switch to open the Ore area right next to it.
2/4 After hitting the switch and starting the data board quest, go to the path to the left (when facing the triforce tower). Turn around from the switch to activate the portal and you will see a switch above some ore. This activates a small elevator which you can ride and jump over to the secret.
3/4 After clearing 2 of the portals, you will ride an elevator up. After moving across the bridge a bit, turn around and look up and to the left. Shoot the target and go into the area it opens.
4/4 In the back of The Archive, there is a switch up on the wall. Shoot to reveal a secret.
Progenitor
1/5 When you first get scanned to enter the structure, turn around. There is a secret area to jump to on the right.
2/5 In the room where you fight the first Harbinger. Go to the right up the stairs to the back of the room. There is a small ledge you can jump to from here which will open and reveal an armor pick up.
3/5 After the 2nd Harbinger, you'll go through 2 portals and be at the top of a very long ramp. Carefully drop down right in the middle at the start for a secret.
4/5 After the 3rd Harbinger, you will come out a tunnel and shoot two yellow targets right next to each other, than another 2 on pillars to lower the sand. Turning around to face the nexus point, there is a small room on the left side next to a yellow glowing door. Secret is inside.
5/5 On the opposite side of the nexus point from secret 3, go towards the back and jump up the level here to find 2 ammo pick ups that are secret.
Hexarchy
1/2 After clearing the main room, the floor falls away. Before dropping down, jump onto the largest raised area (it does not have an ammo refiller) and then jump to the small nook on the rim of the wall. Some sand falls away to reveal an automap.
2/2 Right before the white exit portal, jump onto a ledge to the right with an ore and some pickups.
Trench
1/5 Directly at the beginning. Jump on the pillar with the blue diamond on the left.
2/5 After going down the elevator and grabbing the nexus point, jump up to the ledge on the right and just follow it to the end.
3/5 Behind the second switch you press when coming back outside (on the island with the nexus point). Drop down to find it.
4/5 In the room where you turn the beam to the right, on the left side from the switch there is a faintly glowing switch you can activate.
5/5 After you turn the beam to the right, you’ll enter a large room where you fight 3 harbingers. On the right side, you can walk up a narrow ramp to jump over to a secret ore and chaos ammo.
Space Station
1/4 Kill the 1st harbinger and ride the elevator up. Underneath the little bridge is a secret ore - just jump down to the side of the bridge to access.
2/4 Before activating the switch by the nexus point to go down to the glass walkway, go to the right. The computer screen on the middle of the right was is activatable.
3/4 After going through 1st ice room, in the room with the nexus point is an ore with a target you must grenade launcher
4/4 After the ship pulls the wall off immediately after the previous secret room and you go outside, do not activate the switch and keep going around for a secret ore
Aftermath
1/4 First area directly in front-right of you. There is a cliff with fire on top. Jump up and walk around fire to find a secret ore
2/4 Still in the first area, there is a secret ore inside the cylindrical piece of station in the middle. To the right or left of its green door is a small gap you can enter through.
3/4 Still the first area. Facing the green door from the previous secret, turn around and jump up the platform to the left and go inside to find a secret ore by the back window.
4/4 Move through the level until you come back to the starting area, but are now on a much higher ledge. There will be a nexus point. Jump to the platform to the left of the nexus point, then the right, then back over to the front left where there will be some armor and ammo pickups. This ledge is secret.
Frost
1/4 First area. On your immediate left will be a fiend. Jump up to this platform to find a secret armor in the back corner.
2/4 After getting the chaos caster, you will have to melt ice to go down the elevator shaft. On the second ledge down is a partially broken grate - shoot it several times to break it and find a secret ore.
3/4 After dropping down the elevator shaft, you will drop down one more shaft onto a nexus point. On the left side of the next room, there is a platform with some fiends on it. Jump up to find a secret armor behind the center pillar.
4/4 You will enter a room with a nexus point on the right, snow on the left and a chain gunner. Up and to the right is a small hole, jump on the supports in the middle of the room to get up and find a secret ore.
Gate to Chaos
1/5 After trying to ring the bell and failing, a path will open on the right. After a nexus point, you will come into an organic looking room with a yellow skylight. Go down through the middle of the room to find a secret ore
2/5 Continuing down this path, you will step on a pressure plate to open 2 gates and then start to climb up the castle a bit. In the second room on the right at the top of the stairs, a switch is hidden in the wall. Press to reveal a hidden ore.
3/5 Same path - you will cross a bridge. To the right is a yellow room and 6 crawlers. To the left is a tower with a broken wall. Inside the tower on the left are small ledges you use to climb up to find a secret ore.
4/5 Inside the labyrinth. From the start, go left after 2 dead ends on your left, then just follow this path to the end to find a secret ore.
5/5 After the labyrinth, you will enter a room with ramps on both sides leading up. Take the ramp on your right up to the top and turn left. There is a door here. Go into the left corner of the door and you'll hear a prompt - activate to open the door and reveal a secret ore. (Thanks to YouTube user Skyrimz_ for finding this one, was a doozy)
Zeromaster has a 100% Speedrun which is useful if my text guide can't find you the secret: