After going through the gate keep going forward until you get to the end of the corridor then turn left and keep following the path.
Enter through the door on the left side when you get to the room with 2 doors. You'll see that a church is burning from the window in the next room.
Now continue following the path and you'll start seeing some people. The guards are trying to "clean up" all of the patients.
Keep walking towards the gate and turn right at the end of the corridor. Open the door and jump over the table. Then continue walking towards the other side.
Turn left at the end of the corridor and go inside the office. There's a folder on top of the desk at the right side of the room. Take it and take the battery on top of the other desk then leave the office.
Crouch down and head through the small hole on the lower side of the barricade and turn left. Continue following the path until you get to the well lit area.
Just keep on following the path, you'll see some dead bodies in the corridor go past them and into the next area. There won't be anyone chasing you anymore so you can run as much as you want to.
Go inside the door on the left and head for the other door inside the room to get past the barricade that's blocking your way.
Go inside the first open door on the right side and grab the folder on top of the table. Then head back outside and keep on walking towards the gate.
Exit through the open door and turn left. You'll be familiar with this place if you played the first game.
Now keep walking until you see the main stairs. Use it to get down to the ground floor.
Once you're on the ground floor make your way to the lobby entrance and you'll find the guy who made you into a test subject. Approach him and watch the cutscene.
Once you regain control of Waylon quickly make your way out of the building and just walk forward until you get to the main gates. You'll notice that there's a jeep with its door glowing red. Approach it and interact with it.
Waylon will pick up the camera one last time and take a look at the source of the black smoke. He'll then drive out of that place.
One last thing to do is to send off the video footage that you have and the game will end.