This walkthrough is intended to get the player through the key points of the game and locate essential items. Any nonessential items and locations will not be mentioned. Feel free to search around as you may find items in locations not mentioned.

The Train -
You start in the Standard Seating car. Head west to the 1st Class Seating. Deal with the zombies and move onto the Bedroom Car and go to the body at the front of the car. Inspect it for a Train Key and a cutscene. Deal with the undead doggies and go back to the Standard Seating car. Use the key on the back door. Go up the stairs to the Dining Room.
BOSS - Shoot him a few times and then run back a few steps to dodge his tentacle arm attack. Repeat until he drops.
After the ending cutscene, go up the ladder at the back of the Dining Room and then move across the roof to the sparking cable. Reconnect it. The person who does so will fall into the opening and be stuck in the Small Kitchen. You can place small items in the dumbwaiter and send it down to the Main Kitchen. Find the key and send it down. Switch to the other person and get down to the Main Kitchen to get the key. Now, go to the Conductor's Office in the Bedroom Car and use the key. Grab the Briefcase and throw the switch. Go up the ladder, head through the Bar, to the next hall and grab the Ice Pick. There's a Hunting Rifle and Shells in the next room, which you might want to grab. Go back to the Bar.
BOSS - Whip out the Hunting Rifle and head back to the door. Let the scorpion get close and aim down. Shoot at it and it should back off momentarily. When it comes close again, aim down and shoot again. Make sure to reload the gun in the menu as the reload animation will leave you open for attack.
Grab the Panel Opener and return to the Main Kitchen, where you need to send the Ice Pick up to the Small Kitchen. Switch to the other person and use the Ice Pick on the door. Now head down to the Main Kitchen and use the Panel Opener on the hatch by the back door. Enter the crawlspace to the Baggage Car. Grab the Gold Ring and combine it with the Suitcase. Go out onto the back of the train and split your team (hit the Start button). Move one over to the lever and the other over next to where the Hookshot is. Have the first character pull the switch and then switch to the other character and grab the Hookshot. Give it to Rebecca and go back to 1st Class Seating. Use it on the open panel at the back of the car. Once on top of the car, move to the opening in the roof and go down. Grab the Jewelry Box and examine it for the Silver Ring, which you'll need to combine with the Briefcase to get the Blue Keycard. Now, join back up with Billy and go to the head of the train, where you'll need to use the Blue Keycard. Once in the Engine Car, select someone to stay (I suggest Rebecca as Billy can take more damage). Once you do, grab the Magnetic Keycard. You have a time limit to get Billy to the back of the train and use the card on the keypad. After which, you'll need to input a series of numbers that equal the random number shown on the display. The game will switch back to Rebecca, who must do the same, except for the fact that her display is damage, so you'll need to keep count in your head.

Training Facility -
After the cutscenes, you can either stick it out and shoot the zombies or you can run for it to the door. Anything you left on the train will be on the floor, so if there's nothing left that you want, run to the door as you won't be back (be sure to take the Hookshot - you will need it again). Go through the sewer and head up the ladder to the Main Foyer. Take the west door on the 2nd floor and grab the Crank Handle. Go back out and take the east door on the 1st floor to the Dining Room. Take the north door to the Boiler Room. Take the nearby door into the Storage Room, where you'll find a Black Statue and a Shotgun. Go up the ladder and head over to the door, which will lead you out into the Lecture Room. Go through the west door and take the hall to the south door, which will put you in the Study. Grab the Microfilm A, split your team and use the Crank Handle on the lift. Take your single team member through the Crank Room, out the door and across the Patio to the north door. Go down the steps and unlock the southwest door. Now, switch to your partner and bring them back to meet up with your first team member. Now, enter the east door and grab the White Statue and Grenade Launcher. Go back up the steps to the larger room and split your team. Have Billy wind the chain and send Rebecca down the ladder to where the cage has been pulled up. Grab the Key.
BOSS - Billy's on his own here, but this fight isn't too hard. Just take a few shots and then move out of the monster's path. You might even find a spot or two where the monster's path will miss you. Be sure to take a shot or two and then tap the R or L triggers to reacquire so that your shots don't miss.
Now that you have the Fire Key, which opens the red doors, you have a few places to visit. Go back to the Dining Room off of the Main Foyer and use the key to get into the Kitchen. Grab the Lighter Fluid and combine it with Billy's Lighter. Now, go back to the Study and use the Lighter on the candle by the door. Go into the Library and have Billy push the bookcase to the side to get the Book of the Good. Examine it to get the Angel Wings, which you will need to combine with the White Statue. Go back out into the hall and open the Red Door at the end. Push the table around and under the Trophy Head. Turn on the light and get on top of the table to grab the Iron Needle. Return to the Crank Room and use the Iron Needle on the clock and set the clock to 8:15 to unlock a few doors around the place.

Go back to the Main Foyer and enter the 2nd Floor door that was just unlocked. Grab Microfilm B and go down to the west door off the 1st floor Main Foyer. Head through that hall to the unlocked door at the end. Use both Microfilms on the projector to get a MO disk. Now, use the MO Disk at the pulpit in the Lecture Room. The code given corresponds to the two desk panels you need to turn on. Split up and move your two members to the separate desks (as marked in the Microfilm slide), turn on one, switch and turn on the second. Now, the doors barred by the knights are open. First up are the doors in this room. Enter the first door you see to find an office with a large chessboard. Look at the chessboard on the desk to take note of how the larger board needs to look. Now, move the King (with the cross) forward three spaces, over one and push it back into the correct place. DO NOT move any of the other pieces, unless you like poison. Grab the Book of Evil and examine it to get the Black Wing. Go back to the Main Foyer and combine the Black Wing with the Black Statue. Place both statues on the scales to open another door. Enter and go to the door at the end. Go into the next room and give Rebecca a boost through the vent into the Torture Chamber. Go to the Power Supply Panel and throw the switches in the following order: Up, Up, Down, Up, Up.

As Billy, you need to haul butt to where Rebecca is. Go back to the Dining Room and go through the back door. Head down the steps and through the Boiler Room. Run past the Primates in the Statue Room and head to the door leading to the room where Rebecca is holding on for dear life (use the map). Go back into the Statue Room and use the lighter on the statues in this order: deer, wolf, horse, tiger, snake, eagle. Enter the first door and grab the Unity Tablet. Head back to the Statue Room and go to the north door and down the steps. Enter the first door and get the Locker Key. Head onto the next door and split up. One person will go up the steps and use the Locker Key to get the Duralumin Case. Examine it to find a code etched in and use that code to unlock it and find Handgun Parts, which can be combined with a handgun to make a Custom Handgun. Next, go over to the control panel and push the buttons to move the gates so the other person can move around and flip the red switch. Grab the Water Key and return to the room with the blue door (where you got the White Statue). In the hall, enter the first door and grab the Vise Handle. Enter the next door and have Billy play the piano. Have Rebecca enter the secret room alone and grab the Battery. Switch back to Billy and have him play again to open the door again. Leave and head to the last door in the hall. In the next hall take the east door and use the Vise Handle on the vise to get the Obedience Tablet. Head back to the Main Foyer. Go out the front doors to the Front Patio, where you'll use the Battery next to the lift. Bring the lift down and have Billy push the crate out and over to the column. Climb up onto it and grab the Discipline Tablet. Grab up all three tablets and go to the knight doors in the room you fought the Large Centipede in. Pass through and place the tablets in the console. Go through the now unlocked doors.

The Church -
Get to the front of the church and split up. Send one of your team over to the side area with the shells and have them stand on the moving tile, which will unlock the front door. Send the other person through, into the Chapel. Enter the door to the Save Room and then exit back out.
BOSS - Make sure to have the shotgun for this fight as the big bat will have some smaller bats aid him. The spray of the shotgun works the best. Let the big bat get close and blast him in the face. If you miss, be weary of him picking you up. If the smaller bats become a nuisance, hit a few of them with a shotgun blast.
After the boss dies, you'll be able to pass back and forth through the door without the hassle of the switch. I would suggest taking the time to move some of your more essential weapons, ammo and healing items from the Training Facility to the Church at this point. It should take a few trips to do so. Once you're ready, give Rebecca the Hookshot and move her to the part of the Chapel where you can see the hole in the roof. Use the Hookshot and go down the ladder to the Back Lawn. Throw the power switch and exit through the gate. Have Billy meet up with her at the now useable elevator. Head down.

Underground Lab -
Go down the hall and open the door. Use the Hookshot in the Reference Room and have Rebecca grab the Leech Capsule and head out into the Upper Hall. Take the last door at the end of the hall. Grab the file and get chemicals from the canister next to the gas-filled room. Go into the next room and get some more chemicals from the green canister in this room. Combine this with the Leech Capsule to get the Blue Leech Charm. Send that down in the lift to Billy and then go out into the Upper Hall and press the switch next to the first door you came out of. Switch to Billy and go out into the hall. Use the Blue Leech Charm on the door and enter the Office to get the Input Reg. Coil. Go through the next door and get the Green Leech Charm. Get back to the Reference Room and send it up to Rebecca, who will use it in the Operating Room. Grab the Sterilizing Agent and return to the gas-filled chamber. Use it on the device to get rid of the gas. Go in and grab the Breeding Room Key. Use the key on the last door in the Upper Hall and run over to get the Dial. Send it down to Billy, who will need to use it on a door in the Lower Hall. Once used, he can input a four digit code, which is detailed in the file you picked up earlier. Have Billy go over to the switch and throw it. Pick up the Output Reg. Coil and switch to Rebecca. Bring her over to where Billy is and make sure she has both Reg. Coils and the Hookshot. Go over to the hole in the ceiling and use the Hookshot. Use both Reg. Coils to turn on the Cable Car. Meet back up with Billy and enter the Cable Car. After the cutscenes, you'll need to go back up to the Control Room and replace the Reg. Coil to get the Cable Car working again. You may want to go back and pick up some essential items to bring with you on the Cable Car, where you'll also find the Magnum. Press on the control panel to head onto the Factory.

Factory -
Leave the Cable Car and head up both sets of steps to the top door. Cross the Lift Area to the small lift and go down. Enter the next door and run around to the end to pick up the Factory Key. Head back to the Lift Area and enter the other door. Use the Factory Key to bring the turntable up. Go out and press on the panel to take the turntable down. Run into the new area and go to the door to start a cutscene. Grab the Elevator Key and head back to where the elevator is (past the turntable). Use the key.
BOSS - This nostalgic monster can be dropped the same way as before. Shoot him with the Grenade Launcher and run. Never stop to shoot in a direct line in front of him. He has a quick lunge attack that you should be able to dodge if you don't stop to take too many shots before moving on.
Go to the elevator. You are on Lvl. 3. Lvl. 1 will take you back to where the Train wrecked in the Facility. Lvl. 2 will take you to a side path that leads to the Cable Car and Lvl. 4 is your next destination.

Treatment Facility -
After the scene, go through the doors and into the office. You need to use the panel to turn on the power to the whole facility. Enter the following points (Top to bottom, left to right): 1) Row 2, Column 2; 2) Row 6, Column 2; 3) Row 6, Column 3. Go down the lift. Pass through the next room and go down the hall to the door at the end. Go through the Pool Hall and down the steps, and then pass though the Outdoor Area to the door. Ignore the puzzle in the Crate Room and go through the door, down the steps and into the next room, the Remains Room. Now reunited with Billy, go back to the Crate Room and send Billy down into the crate area. Push the gray crate down (away from the ladder), switch to Rebecca and have her turn the gate right. Push the topmost crate over. Climb on top of the crates and get around to where you can push the gray crate all the way back. Have Rebecca turn the gate left. Now, push the second wood crate forward and down. Turn the gate right again and have Billy move the crate all the way to the end. Get him out and fill the area with water. Cross and take the Handle. Return to the hall before the Pool Hall and use the Handle on the door. Enter the room and go up the ladder. Go to the canister and get the Red Chemical. Go back down the ladder and go through the east door. Pass through the hall and enter the Bunk Room. Go out the back door and pass through to the next door. Cross over the bridge and enter the Gondola Room. Go down the lift and run around to the other end of the room.
BOSS - He's back! This time, hit him a few times and then run for the next corner. His lunge attack can be damaging if you're not out of the way, plus it'll knock you down.
Press the button and go up the ladder. Grab the Motherboard and return to the Gondola Room. Use the Motherboard and send Rebecca across in the gondola. Now, have Rebecca turn the lever to allow Billy across the damn. Have Billy return to where they fought the last boss and exit through the door. Run over and cross the dam to the other door. Go to the north door in the Turbine Room and go up the steps in the Specimen Tank Room to the Computer Room, where you'll find the Industrial Water. Take the south door to meet up with Rebecca, who will need to get the Blue Chemical from the canister in the Computer Room to make Sulfuric Acid. The north door leads back to the Remains Room. Once back with Rebecca, go back to the Specimen Tank Room and boost her up to get the Battery. Now, mix the Sulfuric Acid with the Industrial Water and combine it with the Battery. Go all the way back to the Outdoor Area and use the Battery on the Forklift. Put one of your team on the crate and turn on the forklift to send them up to the Magnetic Card. Now, go back to the Turbine Room and use the Magnetic Card. Go through the door and run down to the Incinerator Room.
BOSS - Hit him with your strongest stuff. Make sure to hit him a few times and then move on to the next corner. You don't want him to get too close as he likes to pick up and bearhug people. Also, he has a lash attack like the Leech Zombies. Just keep shooting and running. He should fall soon.
Pick up both Shaft Keys and split your team, so that each one has one key. Have one person use their key on the left panel by the elevator and then switch to the other person and have them use their key. In the next room, go over to the huge lift and go up.
BOSS - At the start of the fight, just keep plugging the beast and back up when he crawls too close. After the cutscene, you need to use Billy to distract the monster and key it away from Rebecca, who will have to turn the four cranks. Just get behind or to the side of the beast and shoot it a few times to get it to follow you and then move away from where Rebecca is. If Rebecca gets injured, switch to her in the menu and heal her up, but be sure to switch back to Billy and keep the monster's attention away from Rebecca.