Powering Up the Elevator
Head all the way back to the waterfall (the area just before the Guardhouse entrance). Use the Battery near the elevator and take it up. Open the orange gate on the opposite side and use the Square Crank on the divot to store all of the water in the nearby pool.
Go back to the elevator, take it down, and proceed down the ladder hidden behind the now defunct waterfall.
Back to the Guardhouse (Rebirth only)
If you read Eric's letter, you'll know that a very important book was left inside the Guardhouse, which is our next objective. Go to the Guardhouse and head inside the safe room near the entrance. Take some healing items and save the game if you'd like, and then go to the room where you fought Plant 42. Instead of finding the carcass of the plant you fought before, you'll find the Yawn, who has made the Guardhouse his new home. Surprisingly, this is just a knife fight, and a long one at that.
As soon as the Yawn tilts his head back, this means he is about to strike you. When his mouth gets close, slash upwards with your stylus and keep hitting his mouth with the stylus until he goes back to his original position. Rinse and repeat until he's down. This fight is all about timing when he tries to attack you, so just take your time and he'll be gone in no time. Take the Doom Book Vol. 1 from the middle of the room and open it to find the Eagle Medal. Go back to the safe room, drop off the Eagle Medal, and re-trace your steps back to the Waterfall and descend the ladder.
Lots of Tunnels
Go through the metal door on your right. Jill players will encounter Barry. If you're going for the bad ending, have him lead the way. Otherwise, take charge and go through the door at the end of the hallway. If you're playing as Chris, take the Flamethrower from the wall and open the door at the end of the hallway. Inside this room you'll find a First Aid Spray and some Explosive Rounds (for Jill) or Shotgun Shells (for Chris) on top of the generator on the north side. When you're done taking the items here, head through the metal door on the east side and run all the way down this hallway, where you'll meet Enrico.
After the cutscene, check the corpse for a Beretta Clip (Director's Cut and Rebirth) or a Hexagonal Crank (Original). Proceed back to the entrance and be prepared to fight a Hunter (Director's Cut and Rebirth only). Director's Cut and Rebirth players will find the Hexagonal Crank on the ground just up ahead. Exit the room (Rebirth players will have to deal with a knife fight) and take a left, going through the door at the end of the tunnel. Head to middle of room (Chris players must place the Flamethrower back on the display) and quickly open the door, dodging or killing any Hunters in the process.
Take a right and go all the way down the tunnel until you reach a hole in the ground. Use your newly-found Hexagonal Crank on the divot on the left to rotate the nearby wall, granting you access to the next area. Open the door on the opposite side and walk up to the nearby boulder (Chris players must pick up the Flamethrower on the display). Turn around and boulder will start to roll towards you, Indiana Jones style. Run back to the entrance and wait for the boulder to pass, and then go to the area the boulder was located in. You'll find some Flame Rounds (for Jill) or Magnum Rounds (for Chris) on a shelf in the corner. A hunter, however, spoils the fun and starts to head toward you, so take him out. Once you do, go through the double doors at the end of the hallway.
The Black Tiger
Arachnophobiacs beware, as you'll now have to fight a Spider boss. Jill can easily take him out with just one or two shots from her Bazooka loaded with Flame Rounds. Chris players can use the Flamethrower (which should be enough) or their Shotgun.
Once he's dead, a bunch of miniature spiders will emerge, so either stomp on them or just avoid them. Rebirth players can destroy the web that's blocking the door simply by pressing and stabbing, but other versions will have to pick up the Combat Knife in the corner and destroy it.
Getting to the Lab
In this hallway, Rebirth players will have to deal with zombies while others just have to worry about simple falling snakes. Take a left and open the door at the end of the hallway, which leads to a safe room (yay). Drop off everything except for a weapon and its set of ammo, the Hexagonal Crank, and the Eagle Medal. You can find a First Aid Spray and some Ink Ribbons on the table and a single Blue Herb in the corner. Rebirth players can also find another blue item box puzzle; to solve it:
Your reward will be Magnum Rounds (for Chris) or Explosive Rounds (for Jill). Exit the room and head through the door on the other side of the hallway. You'll see another hole in the ground a long with a divot on the left, so you know what this means. Rotate the wall with the Hexagonal Crank three times and you'll notice a passage on the left with a door. Go through it and get ready for a simple puzzle (Rebirth players will have a knife fight here). Go to the statue in the corner and keep pushing it to the right until it's in front of a differently-colored section of the wall (it's brighter than the others). Use your Hexagonal Crank on the divot to make a wall emerge and push the statue. Use it again to make the wall go back to its original spot, and then push the statue until it's over the small panel in the ground.
Once it is, you'll notice a hidden compartment open with the Doom Book Vol. 2 inside. Take it, open it, and retrieve the Wolf Medal. Exit the room and walk up to the boulder on the other side. Turn around and quickly run back into the alcove to dodge the boulder, and take the MO Disk and Underground Map from the area the boulder was in. Head south and take the elevator up to the surface, where you'll notice a large fountain. Take the sets of Green Herbs and Red Herbs if you'd like and then place the two medals in their respective areas on the sides of the fountain. This will cause all of the water to drain and reveal a hidden staircase and elevator. Head down the staircase and elevator to reach the final area of the game, the Laboratory!