(1) This may well be the very best level of the entire game, with a lot of variety to it and plenty of secrets to figure out. Unfortunately, the only way to score 100% for SECRETS is to do (almost) everything in exactly the following order, which takes away the fun of experimenting with different routes. I found at least 2 alternate routes that required less backtracking, revived fewer dead aliens, and made more efficient use of the powerups (particularly armor), but that only scored 66-83% for SECRETS even though absolutely every secret was fully explored. Here's the by-the-book route: Open the entrance door and cautiously work your way forward along the left-hand row of lockers.
(2) As you reach the gap in the lockers, you will be able to see a "frozen" warrior ahead on the other side of the lockers at the far wall. Move forward just enough to get a clear shot (you can shoot pretty close to the corners) and grenade him so that he's gone for good (remember--it takes a direct hit). Now pivot 90 degrees left and peer around the corner through that opening in the row of lockers; sidestep until you see another "frozen" warrior ahead past a gap in a second row of lockers. Sidestep cautiously so as not to "activate" the enemy, and then use another grenade as soon as you have a relatively clear shot.
(3) Go back to the row of lockers that was on your right when you exited the entrance door. Stand in front of the lockers with your back to the stairway and fire away with the pulse rifle; the row of lockers will drop and you can immediately grenade the warrior inside. Move into this secret area to grab the acid vest, seismic charge, and med kit.
(4) Time to acquire powerups hidden in the lockers. The second locker in the outside right wall of the secret you just opened contains a clip. On the far wall facing the entrance door, there is a derm patch and shotgun shell in the second and fourth lockers, respectively. Facing the same wall, but to your left and on the other side of a perpendicular row of lockers, await a facehugger in locker 2 and a shotshell in number 4.
(5) Now turn 180 degrees and head forward toward a room with your first 3 eggs in it (on the way get the battery in the third locker to your right past the gap--it may have been blown open when you grenaded your second warrior). Nail the eggs with the shotgun or pulse rifle, and grab the derm patch and flame thrower canister. Now throw the switch.
(6) Run out and stay to your left to grab a pulse rifle on the pedestal you just lowered; 2 facehuggers are guarding it, though. If you miss the lift, keep trying.
(7) Now go up a small stairs on your left into a small enclosure containing 2 derm patches and 3 crates. The right hand crate holds a special 200-round pulse rifle magazine (twice the normal number of rounds) and a shotshell, while the left crates house a flame thrower canister and a clip.
(8) Move out via the stairs and stay left into a room with 3 crates. The middle one has a 'hugger ensconced within, while the others hold 2 batteries and a shotshell. Go back out and continue forward.
(9) The wall on your right will have a facehugger sitting on it near some barrels. Aim up with the pulse rifle and nail it from afar (get too close and this 'hugger might just jump down and come after you!). Just ahead past the barrels a warrior is standing; try to activate him and blow 1 of the barrels as he runs past it to kill him. Now blow the remaining barrels. You may notice 3 crates sitting against this side of the tower; DO NOT BLOW THEM NOW or (for some odd reason) you will not obtain 100% for SECRETS at the end of the level.
(10) Move to the other side of the tower and destroy 2 hard-to-see eggs hidden behind the crates there. Throw the switch where your path dead-ends and run around the tower, staying to your right (NOW is the time to open the 3 crates and kill the 'hugger inside each). You have just activated the lift you will dead-end at, as well as the 2 warriors guarding the tower.
(11) Step onto the lift and then back up and drop off it; the 2 warriors will run out onto the upraised lift when it reaches the top. Rarely, 1 of the warriors may jump down off the lift to get you, but most of the time you can take them out safely with some very high-precision shooting. Aim the pulse rifle up as high as you can and back up until you can hit the aliens (this is so far back that they just disappear into the darkness--you can try turning the brightness higher on your television set for this maneuver). Each will take 3 direct hits to kill. You will probably waste some shots making sure you are back far enough and lined up properly, especially on HARD difficulty where you cannot see where your shots are going. Your sniping successfully accomplished, go back to the switch and lower the lift again. Now ride it up to the tower.
(12) A flame thrower canister is sitting at the top when you arrive. Ignore the 2 switches unless 1 of the 2 lifts ahead are down; the left switch will raise the near lift and the right switch the far one.
(13) Now run straight ahead to the battery switch (each lift starts to drop when you run across it), and then wait for the far lift to hit bottom behind you. Now activate the battery panel and the lift behind you will come back up (jump off here and it will cost you 15 health points no matter how much armor you're wearing!). You have just opened the exit doorway. Step onto the lift to go down, and prepare to kill a freshly-materialized warrior awaiting you.
(14) Now head back to the stairs opposite the first secret on this level. Any previously-killed facehuggers will be revived and ready for a second round, and you will find 2 newcomers joining them as you go past the lockers. If you killed 1 or both of the facehuggers on the pedestal so that their bodies rode the pedestal back up, you are probably safe from them (although they may look like they are right next to you on the motion tracker). I did, however, have one jump off the pedestal and come after me once. Got hugged, too. Leave nothing crawling and go up the stairs.
(15) Kill the warrior at the top and then go down at the other end by picking your way down the collapsed walkway. You are now in the second "stage" of this level.
(16) Head off to your left toward an opening just past some crates hiding a switch. Inside are 4 facehuggers; zap them before they scurry to places unknown. Exit, go past the raised pedestal, and then turn left to face another opening in a wall. There is a warrior just inside. Dash in to get his attention and then back up immediately; he should come straight out at you and offer an easy grenade shot.
(17) With all the animate enemies in the immediate area vanquished, go back to the switch behind the crates. Blow the crates (the right-hander will release a 'hugger), flip the switch, and run to the pedestal to grab the acid vest and (if you need it) the med kit. This particular lift works only once, so don't miss it!
(18) Now head back to the facehugger room and open 3 crates inside; 2 hold facehuggers while 1 contains a med kit and clip. At the opposite end of the room are a derm patch and shotshell on the countertop.
(19) Exit and go to another switch out in the open, opposite the pedestal switch. Activate it and rotate left to meet the warrior that rushes out to greet you.
(20) Kill him quickly and enter the room he came out of before the lift goes back up or you will not be able to get back to this location. It is best to enter this room and deal the final blow there so he remains trapped below ground rather than reviving on the lift to cause grief later on down the line. There is a second warrior in the room, too, and you will definitely take some hits while doing this. More armor is on the way, but try to keep the damage to a minimum. Now, blow the crates. One contains a facehugger (bad), but the others contain a seismic charge, grenade, and med kit (good).
(21) Throw the switch to reactivate the lift; move onto it, and turn right to go into a second secret room. Inside are a battery, pulse rifle magazine, and 9mm pistol. You can back out immediately onto the lift to go up or, if the lift has already left, flip the switch to bring it back down again.
(22) Now move into the room that the warrior you grenaded came out of. Inside are a battery, 9mm pistol, shotshell, and derm patch. There is also a switch that lowers the forklift platform just outside, but don't touch that button just yet! By now, your activities should have aggravated a warrior on the walkway above you, and he should be standing on the raised forklift platform just waiting for you to lower it. Aim up with the pulse rifle and grenade him if you don't want to deal with him 2 more times later on.
(23) Now flip the switch and move onto the platform. It will raise you up to the walkway, and there are 2 shotshells on it if you need them.
(24) Move down the walkway and turn on the switch you will see immediately to your right. This activates a lift further down on the walkway, at the second gap in the railing. When the lift starts down, face right because 2 'huggers are preparing to jump you.
(25) After eliminating them, get the flame thrower canister and battery. Throw the switch and the lift will come back down.
(26) Run ACROSS it into another room with lots of crates. It is easiest to deal with all the facehuggers next door by blowing the 2 right-hand crates (the first holds a med kit) to create a small gap. Stand near it and dispatch the critters as the come for you. Now blow the rest of the crates to find a seismic charge, 2 shotshells, and a pair of facehuggers.
(27) Continue into the freshly-opened room and blow the crates at the far end--a residual facehugger may be hiding behind one. Don't miss the 3 derm patches here.
(28) Now exit the room and face left. Go past the upraised pedestal to a stairway leading below ground. (There is a second pedestal on the other side of this recess; this one comes later). A warrior will emerge when you approach; grenade him now or pay for it later. Downstairs will be a battery and a switch. Activate the latter and run up the stairs back to the pedestal. On it are a shotshell, a seismic charge, and 2 facehuggers. You may have to try several times before catching this lift--it's one of the faster ones in the game.
(29) Before you head back to the forklift, there is a small enclosure in the immediate vicinity. The stairs into it are blocked by 2 crates--you know how to fix that. Switch to the flame thrower and start firing before you step down into this area. Two or 3 facehuggers (depending on where that one you shot off the top of the wall landed) will be very ready for you, and you may end up getting 'hugged despite all your experience and your very best efforts. Inside are a med kit and flame thrower fuel. If you are careful not to step too far forward when entering this enclosure, you can toast the facehuggers and then grab the flamer canister; this saves you from wasting fuel. Sometimes when walking near this "room", 1 of the facehuggers may surprise you by jumping over the low threshold.
(30) The walls to either side of this enclosure come down when activated: walk straight into each wall right in front of the shotshell on top and the wall comes down so you can grab the ammo. Be careful not to let any revived enemies come over from the other side! It is best to re-raise the wall by running over it and then immediately backing up (but don't go too far or you will be trapped on the other side!). If nearby aliens have been disturbed, watch your motion tracker to see when they are farthest away and then go for it.
(31) Now go back up the forklift, watching for the reawakened facehuggers certain to be waiting for you along the way.
(32) Continue forward on the elevated walkway to the stairs and go down. On your immediate right as you hit bottom will be a warrior behind some crates. Try to lure him out after you so he will follow you up the stairs where you will have a quick chance to grenade him. This done, go back down the stairs and very cautiously move forward. There are 3 warriors ahead: try to activate each of them one by one and then serve it a grenade, hot. You may be able to move cautiously enough to get an easy shot at a "frozen" warrior or 2 that hasn't started moving yet. Now calm down and move into the recess back at the bottom of the stairs; the switch here will enable another lift on the walkway you came down from. There are also 2 clips here.
(33) Go back up the stairs, and about halfway back to the forklift will be a gap in the railing; step on the walkway here and it lowers you to a secret room containing a pair of grenades.
(34) There are 2 switches in this room. The right switch (as you enter this room) lowers the second pedestal near the underground stairway you encountered earlier.
(35) The left switch will lower the part of the walkway you just came down on; run across it and then left to re-enter an "old" part of this level and get to the second lift. This one stays down, and on it are a pulse rifle magazine, acid vest, grenade, and flame thrower canister.
(36) Now work your way back to the forklift (again--I told you there were more efficient routes!), killing any revived facehuggers along the way. Proceed up the forklift and back along the walkway to the stairs and go down.
(37) In the second recess on your right (past the switch in the first recess) are 2 clips, and in the third rest 4 derm patches. In the left recess are 3 crates. Blow them and grab the 2 shotshells and flamer fuel inside if you need them; if not, you'll be coming back this way again and you'll definitely be able to use them then.
(38) Now move forward into the next area. This is the APC garage, and you can get a pretty good look at these vehicles once you kill the 'huggers. As soon as you enter, 1 facehugger will rush you from the right: kill it and rotate to knock off the one coming up behind you. Now stay left to work your way around the APCs. The shotgun or flame thrower are the only 2 weapons to use here, because the facehuggers jump out from under the vehicles and you have only a split second to fire. With either choice, it's a lot harder to miss. Four 'huggers will jump you as you work your way around these first 3 APCs. A fifth may come up from behind you--watch for him on your motion tracker. [A CURIOUS NOTE: I was backing away from a facehugger into the corner formed by the front left of the first APC when I actually hopped up backwards on top of it! I was so surprised that I immediately fell off. All my attempts to duplicate this accidental feat have failed. I may have fired the shotgun, giving myself an additional boost, right when it happened.]
(39) After working your way around the third APC, you will see a switch ahead. (There is also a second forklift near here; this one doesn't do anything). In the recess to the right of the switch is a seismic charge; when you grab it, a facehugger nearby will detect you and come running. After killing it, activate the switch, which enables a secret lift.
(40) Walk onto the lift (you can see the outline of it on the floor, with one edge against the wall on your right between 2 rolls of wire) to lower it. A warrior will charge out of the secret room at you soon after you are down. After eliminating him, blow all the crates. Save the barrel for last unless you want to deal with the first 3 facehuggers all at once. Also inside the crates are flamer fuel, 2 shotshells, a clip, a seismic charge, and 2 med kits. The right-hand crate against the far wall contains a final 'hugger. Now activate the switch and move back onto the lift.
(41) Once up, move straight forward and around to the left of APC number 4 (you actually saw the back end of it while working your way around the first 3 APCs). Go forward until you reach a wall; 2 to 3 facehuggers will challenge your presence along the way. At the wall go right, back to the shotshells and/or flame thrower canister you saved (or didn't save) just before entering the APC garage area. You will probably have to kill a revived facehugger or 2 to get them.
(42) Now move back along the wall in the other direction to the exit doorway. This was a long one! Unfortunately, if you did the secrets in any other order, you get less than 100%.