Level 18 - Floating Fortress (6 secrets)
1. Once on the boat at the start of the level, maneuver it to the right side platform. JUMP onto the right side platform. Hit switch behind crates. Door should start sliding back and forth. JUMP on tallest crate, then JUMP other side. Then JUMP on crates on other side. JUMP on the sliding door. Door should bring you back to a chamber. BLOW crack open, SHOOT switch. Inside room, get nuke, rail rods, missiles.
2. In flooded naval vessel, in room before snake boss, there is a dead body wearing blue pants. STAND facing him and with the window behind him in-line. Back away and SQUAT down. There is a place that can be dived into get medikit.
3. In huge naval vessel, GO up to bridge (control centre of ship). GO to the weapons station. USE the turret and position the barrel so that it faces West. Then GO outside. JUMP onto the cannon and walk on the barrel and JUMP into the airvent.
4. Inside lower level of the naval vessel, in bedroom with "Jolly Roger" (pirate flag) on wall. OPEN/USE "D. JONES" locker, then use the wall inside, leads to other room. USE girl until she gives you a random item. If you kill her you don't get an item. OPEN the other locker "C. Hook" to get guardian head.
5. Reactor room (where you turn the power on). USE the PC monitor, control panel opposite room opens. Get cookie, armour.
6. Room after rail gun turret, up ramp. You should be able to see a small gap in the floor with items inside. BLOW up the wall directly above it to widen the gap. Then SQUAT and walk against wall the blast should be enough to widen the gap for you to drop down. Get guardian head, cookie.
Level 19 - Water Torture (6 secrets)
1. Bedroom with vacuum cleaner. Between the second and third bed, there is a door. Flood the chamber by SHOOTing the tanks by the window. Only after room is under water, can you open this door. Get nuke. Float up and shoot the 2 airvents and get the red key and sticky bombs.
2. Room with 2 columns on a "light red" platform. Turn light on (USE light switch) column will sink. Get rail gun.
3. After using "mini laser tank" to BLOW open metal door and a hole in the far wall infront of you. GO allow way up and outside to where the submarine is circling the island. If you look at your overhead map, GO to and face the Northwest "red" pillar/chimney, SINK down and GO through the hole in the wall. Get guardian head.
4. After getting yellow key, GO to "lift with yellow key" and go downstairs. Exit the lift and send the lift back up. Panel to the East should open. Get ripper heart, cookie.
5. After getting the blue pass key, GO to "blue corridor". Northeast corner has panel that can be opened. Get kevlar armour, smoke bomb.
6. I took 3 hours, jumping, diving in diving out before I figured out where this secret was. Guess where this secret is. Go ahead. Take a good guess. Yup, its had to be in the last place you would look, behind the level end symbol. Get a heat seeker card.
Level 20 - Stone Rain (5 secrets)
1. After killing the Fat boss, JUMP into the Large picture behind him. Get 3 cookies.
2. Entrance to Fat boss's "house". JUMP against (make sure you push against the wall) and USE the "tiger" picture on the right side (Western side). Panel next to it opens. (IMPORTANT: I think there might be a problem with getting out of this room. The button inside doesn't seem to work so you might get trapped inside. I'm not sure if its a bug or there's something else you have to do. For the time being, just go in and get out before the door closes.) Get heatseeker card, armour, caltrops.
3. Halfway on the footpath to the Fat boss's "house", there is a crack in a wall opposite the path (facing Northwest). BLOW it open and JUMP in. Get nuke, etc.
4. West of slope down to snake boss, around the to small "snake face" on the wall (the one WITHOUT the rotating thing). To the left (North) There is a panel that can be USEd. Get 2 nukes.
5. Before final boss when walking on grates, you should be able to see a nuke under your feet. USE the wall on the left (North) to get it.
Non-secret things to note:
If you get the nuke in secret #5, you can keep walking on the lava around to other chambers and you should come up to a place where are 2 killer bunnies and 4 dead "Mutant Ninja Turtles".
(Source: http://www.pcgameworld.com/ Website)