Secret #1
In the pachinko area, where an explosion reveals a way inside the crashed airplane, if you look to the corner of the pachinko machines closer to the wall and the airplane, you'll spot a small switch. Use it to open a secret panel on a wall on top of the machines.


Secret #2
On your way to the Red key, there's a room with three phones, three pachinko machines and a couple vending machines. If you look up, on top of the snack machine, you'll notice a closed metal door:

In order to open it, go to the Red key locked elevator. Unlock it, call it once to have it come down and then call it again to have it go down another floor. This will cause the metal door to open, allowing you to enter the duct and get the secret.


Secret #3
Instead of using the elevator, follow the conveyor belt near it. On your way, you'll cross a dimly lit room with some enemies. Notice the crusher nearby with a switch right beside it. Pressing the switch will open a panel inside the crusher. Get into it for the secret (be careful not to get crushed when going for it).


Secret #4
Continue from the conveyor belt, collecting the Yellow key on the way. Go to the Yellow key (and the elevator) room, and look for an entrance with stairs leading up. Head up those and, when on top, go to the nearby bookstore. Stand in front of the cash register and activate it to make a panel right in front of you slide revealing the secret.


Secret #5
Before going to the Yellow key door, go towards the Blue key door and, after passing the metal detector, move to the right to reach the "Blue Brews" bar. Inside it, notice the sign hanging on the wall with chinese (probably) writing. Jump and activate it to make the wall next to it slide and reveal the secret.


Secret #6
In the control room with the Blue key, notice the soda machine in here. Jump on top of it and look towards the side of the big radar screen. You should notice a button (unfortunately, none of my screenshots came nicely, so you'll have to believe me and look for it =( ). Shoot it and the wall behind you'll slide, revealing the secret.


Secret #7 + Secret Level
Finally, go back to the level's elevator and take it to the higher floor. Then, leave the elevator, press the switch to send it back down and quickly jump on top of the elevator's ceiling (you gotta be quick since the doors will close as soon as the elevator hits the other floor). Afterwards, press the nearby button to bring the elevator back up. With this you'll be able to reach an air duct which takes you to both the secret and the secret exit.

Secret #1
When you reach the big metal door that leads to the center of the level, notice the four phone booths nearby. One of them will be darker than the others. Use it and the soda machine next to the phones will slide revealing the secret.


Secret #2
After entering the Blue key door, look to the right to spot a small reception room with a computer. If you use it, the archive cabinet behind you will drop, revealing the secret.


Secret #3
Near the last secret is a red car, with water behind it making artificial waves. The hole between the water and the wall can be crossed, and on the other side is a secret.


Secret #4
Still near the last secret, go to the next exposition room, with a red pickup:

The wall closest to the backup of the pickup is slightly off-center and darker than the rest. Press it to open the secret.


Secret #5
Right next to the last secret is a very obvious crack in the wall. Explode it to reveal the secret.


Secret #6
After entering the room opened by the Red key, of you turn the lights in this room off, the bookshelf near you will drop revealing the secret.

Secret #1
In the room with the Red key, go to the adjacent room (which you probably jumped into to reach this part of the level), which has a computer using a Shadow Warrior wallpaper. Use this computer to make the machine with the Red key drop, revealing the secret.


Secret #2
Afer unlocking the Red key door and crossing the small corridor, you should come to a room with a ramp to the left. If you look up, more or less to the middle of the wall, you should spot an air vent. Open and enter it for the secret.


Secret #3
In the room with a computer and an aquarium in front of it (beyond the Blue key door), if you use the computer, a secret wall behind you'll open revealing the secret.

Secret #1
At the first crossroads you reach, take the left route. Soon you'll see a lava river: the wall from where the lava comes from can be opened to reveal the secret.


Secret #2
Go back to the crossroads and take the other route this time (the one that leads to the Blue key). Let the explosion seal off the way forward. Notice the hole the explosion opens on the wall: you can cross it to get the secret, but be aware that standing in this area will hurt you!


Secret #3
After going down the elevator and using the Blue key, go foward while keeping an eye out for a drilling machine to your right. On the wall behind it is a crack. Blow it to reveal the secret (it will take you back near the Blue key door).


Secret #4
Right after escaping the moving drilling machine trap, be on the lookout for a crack in a nearby walll. Explode it to reveal the secret (which includes a stair that takes you back to the upper floor).


Secret #5
Near the end of the leve, you'll see two fans, one which isn't working (and provides the way forward in the level). Enter it and use the switch to throw you up to the level's last area. From here, If you jump into the other hole you'll fall on the back of the working fan, which is the secret.

Secret #1
After passing the corridor accessed by the Blue key door, you'll arrive at a large area, with the machine gun turret and the locked Yellow key switch. Move to the right area, the one with several stacked boxes. There will be some boxes stacked forming a stair nearby. Going to the back of these boxes (where a Medkit and Riot gun rests) counts as a secret.


Secret #2
Still in the same area as the last secret, look for an emergency light at ground level, beside a stack of boxes and near the edge of the level. You can walk behind it, circling the wall, to arrive at a small ledge with a Missile Launcher (visible from the corridor you crossed to arrive in this area). This area is the secret.


Secret #3
Still in the same area as the last secrets, climb the stair-like stack of boxes. When on top, jump to the nearby stack of boxes (the one without the Fortune Cookie). And look towards the side of the nearby wall: you should notice a Rail Gun Rods. Jump to this small ledge to get the secret.


Secret #4
In the area with the rigged submarine, operate its turret and blow up the crack in the metal door in front of it. Then, move to the hole opened: in the hole, the wall to the left is hollow, and a Ripper Heart lies inside. Enter this small hole for the secret.


Secret #5
Still in the same area of the last secret. When on the ledge that contains the Yellow key, look for a nearby stack of crates that can be jumped to towards the submarine. Once on top of it, look for another stack of crates, from which an enemy was previously shooting at you. Jump to it to get the secret.

Secret #1
After opening the Bronze key door, to your left will be an opening with a pipe and water flowing down from it. This pipe can be climbed and, at the top, is the secret.


Secret #2
From the last secret, continue through the corridor and enter the bathroom to the left. Inside it, use the mirror to make it slide and reveal the secret.


Secret #3
Continue the level until you reach a room with two beds, notice that one of the wall panels in the corner doesn't go dark like the others. Use it to make it slide and reveal the secret.


Secret #4
Continue through the door from the last secret. When going through the corridor with a metal fence, there's a portion without this fence where you can jump to. From there, jump to the nearby hole with water and dive down. At the bottom is the secret.


Secret #5
Inside the room with the Red key, notice how only one of the walls have an air duct. Actually the wall opposite to it also has as air opening, with a fake wall covering it. Just jump in it to get the secret.


Secret #6
In the room where you obtain the Silver key, there's a mirror which can be opened to reveal a secret.

Secret #1
At the beggining of the level, use the boat to jump to land, activate the switch to make the gate start moving, and use the nearby crates to jump to the other side of the area. From there, use the crates to jump onto the moving gate:

Once you're on the gate, notice a hole in the wall in the far end. Enter it and you'll notice a crack in the wall. Blow it up to reveal a switch, activate it (by shooting) to make the nearby door open, finally revealing the secret!


Secret #2
After the room where you blow up the boiler, there'll be a drowned ninja body in this room. If you stand beside it, towards the exiting door, you'll be able to dive down into a small hole with a Portable Medkit, which counts as a secret.


Secret #3
In the room with the Blue key, you should see a small hole with some goodies inside. In order to be able to enter it, shoot an explosive weapon a few times against the wall: this will make the wall deform to the point you can squeeze into the hole and get the secret.


Secret #4
After using the Blue key and entering the ship, go up the stairs to the bridge. There, control the ship's turret and turn it 90 degrees to the left, so that the cannon's pointing to the left wall. Then, go back outside, around the ship, and jump on top of the cannon.

Look up and notice the air vent on the wall. If the cannon is aligned enough (if not, you'll have to go back to the bridge to manouver it), break the vent and enter the duct for the secret.


Secret #5
On your way to the Yellow key door, you should spot a bedroom. Enter it and notice the 3 lockers on the back of the room. Open the middle one, named "D. Jones", and then open the back wall of the locker to reveal the secret. Also, talk to the girl inside the secret to earn the "In the name of the moon" achievement.


Extra
In the small corridor before the ship's generator room, there's a crack in the wall. Blow it up to reveal a Grenade Launcher!


Secret #6
In the ship's generator room, look for a computer tucked away in a corner of the room. Use it and a panel will drop down on the other side of the room (it's in front of a crack in the wall) with the secret.

Secret #1
After opening the Blue key door, in the middle of the blue corridor, notice that one of the panels is blinking: open it for the secret.


Secret #2
In the Red key room, in between the beds is a door, which can only be opened when the room's been submerged. So, blow the explosives, quickly open the door, get the secret, and run for fresh air! =)


Secret #3
In the Green key room, flick the light switch next to the Red key door. Once you do, one of the pillars behind you will drop with a Rail gun. Pick it up for the secret.


Secret #4
After going down the elevator opened by the Yellow key, send it back up (without being in it) and a panel nearby will open, revealing the secret.


Secret #5
When controlling the laser tank to blow up the metal doors blocking your way, you should spot a hole in one of the walls. Explode it and, when crossing this area later, go through the hole for the secret.


Secret #6
The last secret is located right behind the end-of-level switch.

Secret #1
As you go up the canyons for the Sumo rematch, after you pass the first small space, look to your right and down for a crack in the wall. Blow it up and enter the hole for the secret.


Secret #2
At the door to the Sumo boss, notice the tiger motifs on each side of the outer walls. If you jump and use the right one, a panel beside it will slide revealing the secret. BE CAREFUL FOR THE SWITCH INSIDE IS BROKEN, SO IF YOU'RE INSIDE WHEN THE DOOR CLOSES YOU'LL BE UNABLE TO EXIT THE SECRET AREA!!!!


Secret #3
Inside the room of the Sumo boss, the large painting in the back can be jumped into for a secret. Also, you can shoot the boss from inside here without him noticing you, making this an extremely easy fight.


Secret #4
In the room with the Serpent boss, look for a red room with a serpent wall in the back. There'll be a portion of the wall that's brighter than the others. Open it to reveal the secret. Also, as a side note, the pool in this room can be dived into for an assortment of goodies, but since it's lava, you'll have to cross it fast since staying in will hurt you badly.


Secret #5
After jumping into the volcano, as you move in the corridor, look underneath you to spot a ledge with a Nuclear Warhead. The wall directly above it can be opened, giving access to the warhead and granting you the LAST SECRET IN THE GAME!!!!!!


Extra / Easter Egg
Don't just jump back from the last secret. Instead, run to the right through the lava river where you'll find a large secret area . Explore here a bit to find a TNMT reference alongside some "unordinary rabbits"!