Edit: Battlefrank did a video Let's Play. Link:
If some part of the walkthrough is unclear, refer to the video.
The tutorial explains all the mechanics rather well, so I'll just give you a simple tip for dealing with guards. Most of the time, bursting into the next screen and crouching while firing will give you a major advantage and leave the guards no chance whatsoever. However, quite often you will have to climb up or down to get at guards. See if you can jump down on the guards level instead of dangling, thus gaining the advantage of surprise. If you can't – fake them out. Dangle or climb so that the guard sees you, then quickly retreat. The guard will fire into the empty air, then go back into his "relaxed" pose. Once he's done firing, he has to go through several pose shifts before he can fire again. This is your chance to get to his level and take him down safely.
You run into your first guard on the very first "real" game screen. Fake him out as described above and use the keypad next to him to open the door at the top of the screen. Climb up there and exit to the left.
Some plot info on the terminal next to you, a guard below you. Remember this as the "elevator screen" – this is where you have to head at the end of the game.
There's no way down, so just keep heading left.
Take down the guard, and heal any wounds with a nice shower.
Drop down and take out the guard. Head left for some plot info, then come back, take out the guard again, and head right.
Kill guard, take shower.
Toughest fight so far – two guards at once, on separate ends of the screen. Drop, crouch, and turn to kill the other the moment you've dealt with one. Exit right for plot info and write down the code for opening the doors on this level. Return to deal with a single guard, and use the keypad to open a cell door – the number you've just written down followed by 08.
Two screens to the left, passing through the showers, than climb to the upper level and head two screens to the right. Enter the cell, grab the explosive and go all the way to upper left area. Use the explosive, leave the screen, return, pick up the object and head down.
Head right. On the third screen you pass, one of the bodies will reveal itself as a zombie. Just leave the screen to the right – trying to gun it down may well result in injury. On the next screen drop a level and head to the left. Heal yourself at the showers, pick up the key and head to the right again.
Ignore the zombie and head right. You can drop down and get some plot info. Head right, take out zombie, leave the key near the crane and head right again. Pick up the wrench, head back left, drop down, take out the zombie and use the wrench on the machine. Leave the wrench, then go right and right again. You can take out the zombie and head low left for some plot info. Once you're done, drop down.
Head right, grab some trousers, check out the sites below you, then head back up. Go left until you get back to the crane, use the trousers on the part you previously wrenched, pick up the key and use it on the slot, then climb up the crates to get to the terminal and press the button (once!).
Head left to the beginning of the level. You can now drop down into the room with the dead guard. Read the terminal, write down the code, open the door with the keypad and head all the way right. Go down to the gymnasium, and grab the object. Head all the way up, left, up and right back to the elevator room. Make sure you have a nice cold shower along the way.
Your first boss fight awaits. You can save during the fight, but the boss will keep moving, so be quick. Grab on to a ledge facing upwards and look at the boss as it prepares to attack. If it doesn't show little white spikes, you should clamber up, then go back to hanging once the attack is done. If it does show spikes, let go of the edge and shoot at it. If you have the reflexes, the whole fight is very simple.
Congrats on killing that things yellow ass. On to
123 part 2.
First we go through the most annoying part of the game. Just keep heading left, and down, and left, until the cut scenes are over. Then wander about your cell, approaching the door every once in a while until it opens.
Head right. One code to write down at the top computer, one object to pick up at the bottom, some plot info behind the guard. Head down.
Dangling and faking will likely get you hurt here, so just jump down and take out the guard. Go right and repeat the procedure. Get some plot info and press the keypad – once. Press the other keypad to open the door, head right, get your plot info. Press up in front of the panel, use item, pick up monitor circuit. Go back up.
Head right until you run into a keypad, which you will open with the code you wrote down previously. Nothing here right now except for plot info and a shower, so leave the monitor circuit here, and go into the elevator shaft.
Go down. Right. Plot info behind the guard. Bottom right. Right. Down.
You can avoid the first light by crouching and the low light by hanging into the pits. I have no idea how to avoid the light on the next screen – I just run forward, taking some hits. Climb up, and left, hanging from the platforms to avoid the lights. Go up, head right, crouching to avoid the light, kill the zombie and go left.
Grab the item, listen to the plot exposition, then head back to the elevator, up and into the elevator control room. Use the keycard to open the door, open the panel and insert the monitor circuit. Summon the elevator to level 7. Head to the elevator, and climb up (there are handholds on the other side of the shaft).
Head right, have a chat, then head left. Go into the open room, get some plot info and head right again. Kill a zombie, go right again. Another zombie. As you pass the window, you get the best scripted part in the game.
Right, right and down. Down. A boss fight starts.
Basically, you climb on the second platform and shoot at the eye. Whenever a blue spark appears, you climb down. Whenever a blue spark shoots at the top panel, you climb all the way down, to avoid the damaging darkness avalanche. Alternate eyes every once in a while – when one eye is killed, the other becomes a lot more trigger happy. Ideally, you should kill one eye when the other is one shot away from being destroyed.
Congrats on killing that figment of a nightmarish imagination. On to:
1213: Part 3.
The keypad code is revealed after you beat the game. For me, it's always 12721.
Right. Right again. Your first meeting with the patrol drones. They can't be killed, they rush towards you whenever they see you, and they can only be avoided by being on another level / in shadow. Since this train has no shadows in it, you must rush for the opening on top and haul yourself up. Head right, and make sure to crouch whenever the danger sign flashes.
Wait at the edge of the opening until the drone passes to your left, then drop down and run to the right. Go up (in this case, up = roof), right, wait until the drone passes and head left. Touch the keypad, go to the right and up. Drop through the other opening on the same screen, and head right.
Exit the train and head left. Climb up quickly before the drone catches up, or grab the plot info, leave screen, return and climb. Shower, more plot info, right.
Down, take out guard, down, use shadow to hide from drone. Hit the keypad and the terminal. Back up, right, and exit through the next opening at the bottom.
Down, take out guard, right, grab letter and back to the left. Exit – bottom right.
To the right we have a some guards, a shower, and plot info. Middle left there's some plot info, and an id card that we'll use the letter to retrieve. At this point, you can just force your way to the end of the game – go down, rush past the drones taking some hits, hit the keypad and rush into the pit before the camera can turn to spot you, then run past the turned camera into the open door. However, the slightly more elegant version is:
Head up and to the left. Go up, use the shadow to avoid the drone, and use the keycard on the terminal. Write down the code. Head right, down, bottom left. Insert the code, and hit the keypad inside the room. Now head right and down. Use the shadows to avoid the drones and the camera.
Go right, get some plot, go right some more, take a shower. Go right. Prepare for the final boss fight.
Here's how this goes: the middle button turns a light on. The upper button then energizes it. The bottom button discharges the energy. Discharging the energy when the sphere covers the button damages the sphere. Damage it a few times, and it will summon a drone to patrol the bottom of the screen. Damage it a few more times, and it will become much faster. Damages it a few more times, and it will die. In this battle, the fact that the sphere keeps moving when you hit escape while the drone does not is a major advantage – use it.
Kudos on beating the game. Now time to check out the cute secret ending, and consider why the actual ending doesn't make a lot of sense.