You will start the level taking damage from electricity. Quickly move forward to minimize the damage taken. To your right is a room with a Pig Cop in it. Follow the hallway to a door, and open it. To the left of the door is a panel; open it and a pistol and clip will be there. You can use this to kill the Pig Cop in the room. On the other side are two switches.
Press the left switch in the room to the right of your starting position to drop the chair you started in down to reveal a Shotgun, a case of shells, and secret area number one.
The switch on the right will open the curtains to a viewing area with some more Pig Cops and Assault Troopers. Kill them and move further down the hall to a Portable Medkit. Additionally, there are some large medkits in the electric chair room if you need them. Head back to the first intersection and down the hall where a Pig Cop is. Take a left to enter a chapel with some more Assault Troopers and an Assault Captain. Kill them, and take some medkits if you need them. Don't leave yet though.
Stand to the rear of the chapel area, in front of the wooden wall. Make sure you're centered. Face the altar, and look up to see a red button. Shoot it, and an elevator should start taking you up. Look behind you for an Atomic Health and some armor... but don't drop down just yet. You can get another Atomic Health by shooting the hanging person in front of you.
In the chapel, go to the altar and press the open/use key on the center that is sticking up, with the alien face on it. The room should turn red and the cross at the front of the room will flip. Shoot the left pane of stained glass and follow the path. Kill the Octabrain, and go further down the path to an easter egg; the space marine from the video game Doom will be lying dead in front of a Chaingun Cannon!
Leave the chapel and go further down the hallway to three pig cops, lined up. Kill them, and wait for an explosion. Go into the gaping hole in the wall that ensues and up the giant gears. It's tricky, but possible. Once you're up, kill the two Assault Troopers, nab the RPG, and open the panel to reveal the blue access card. Head down to the first gear, and jump past the lower one. You will land on a ledge, and nearby should be yet anther Atomic Health. Head back out to the main hallway and take a left to a caged door. Inside should be a babe, a toilet, a mattress, and a crack in the wall in a corner.
In the room with a toilet and a babe, locate the mattress. Duck in front of it and hit the use/open key. It should slide open and reveal a tunnel; crouch down and enter to find a box of RPG rockets and secret place number four.
Head back to the hallway and pass the opening in the wall. At the end is another Pig Cop and a red door. Kill him, and use your new-found access card to open the door. Head inside to find still more Pig Cops. Take care of them, but don't be too hasty. There is a laser tripbomb on a wall on a metal panel not too far ahead. Crouch past it, jump over it, blow it up with the RPG, whatever it takes. Move on up the ramp and take a left, but don't enter the room quite yet. There are more tripbombs in the door sill, so take care of them with the RPG. Nab the yellow key and shotgun ammo, but be hasty, as once you get the access card, some more tripbombs will start to show up. If you get out in time, you'll be greeted by ever more Pig Cops, so dispose of them in whatever way you please. Head down the other side of the ramp, but again take caution as a tripbomb is stationed in an area similar to the first one. Go down enough to see the Pig Cop, then retreat a bit; he will set it off for you, killing three birds with one stone, as a hole will be blasted in the floor. Go down in to find a fourth Atomic Health. Head back up and enter the door labelled "Control West". Kill the three Pig Cops in the room, and go to the center, underneath the walkway. Fire an RPG up into the door sill to detonate the three tripbombs stationed there; clearly, someone is determined to kill you. Use your yellow key card at the panel down below in this room, and kill the enemies off to the right. Grab the RPG ammo and head out the door on the other side, which opens up to a canyon with many enemies and some turrets, plus some Troopers shooting at you from windows up above. Take care of everything you can, then head to the far left and grab the red access card.
In the canyon, go to the area directly in front of the door you came in from. There should be some slanted platforms. Jump up one, then up to the white area. Be wary of turrets. In the center of the area should be still more slanted platforms. Jump up, then push forward to enter a room with three Atomic Healths. There are also some Pipebombs and ammo for the Chaingun Cannon elsewhere on the platform.
After getting the three Atomic Healths, stay up on the white area. Go to the end of the platform, near where the red access card was. There is a crack on that wall that you can use the RPG or Pipebomb to blast open and reveal some more Steroids.
Head back into the room that had the yellow panel. Use the red access card at its respective panel, and go in. Head up the ramp to see an alien face which will say "Haha! It's too late, Nukem! We're in control now!". There is also a Chaingun Cannon up on this platform. Directly behind this will be a button; shoot it and the room will rotate. There will be hallways to both sides, and a vent shaft in the center above the platform. Avoid going in there just yet, or go in just enough to get the Armor inside and go back. Go to both sides, open the doors, kill the Pig Cops and flip the switches. Go back to the rotating area and into the red door. Assuming you got rid of the laser tripbombs here, it's safe to just head across the platform.
SECRET 7 & 8
Head across the walkway, to a wall with a rectangle on it. Open it up and it will reveal a map of the whole facility. It will also open up two small passageways, off to the sides and slightly up. Jump into these to get some Pipebombs and an Atomic Health.
Drop off the platform, and head back to the main area where you found the yellow keycard. This time, turn to the wall that says "CELL BLOCK 01 02". Just a little down the path, should be a room with tile floors and walls. Go in there and take the boots after flipping the lightswitch to the lights on. Then head back to the lobby. Go down Cell block 01 and kill the Pig Cop, if you haven't already. Shoot the gas container to get a handy shortcut back to a previous room, but you won't need it. Flip the switch at the beginning of the hallway to open different jail cells and find various items. Make sure to check the corners for enemies, because the rooms are designed weirdly. Do the same for cell block 02. However, in the final room, there should be a poster of a woman. There is an opening just behind it, so go into it. Down in here, at the end of the tunnel, should be a few pipebombs on the floor. Pick them up, and throw one. Step back and detonate it. If you look closely you can see a crack on the wall. The same holds true for the area after that one, so blow it up too. The opening will lead to a sewage drain with toxic water; fortunately, you have boots. Follow the drain out to find nothing other than a submarine! There will be a few enemies in the area, so get rid of them. Don't dive underwater just yet though! Follow the path on the opposite side, and kill the two pig cops and grab the Scuba Gear. It'll be helpful for the next level. You can also flip the switch for easy access to the canyon, but you shouldn't need to go there.
Jump up to the slanted platform to the right of the door that leads back to the canyon. Face the wall hit the use key. A secret revealing some Night Vision Goggles should open up.
Head back to the pool of water with the sub and dive in. There is a box of pipebombs on the bottom of the sea, but the focus here is the opening in the bottom of the sub. Head in and take out the enemies if you so choose. Don't hit the nuke button yet though...
Inside the submarine, there is a crate. Behind this crate is a wall. Walk up to the wall and look closely. You will find a door. Use the use/open key to reveal the final secret of the level, containing the sub's engine room and a portable medkit.