The library has a red button that you hit to open the door to a square room with bleachers along each wall, with a invisibility sphere in the middle. 6-8 Chaingunners will pop up once you hit the first step of the bleachers. Best way to survive this is to open the door from the library, run up the stairs, hit the first bleacher and run backwards back out of the room just before the door closes. You can then take your time taking out each of the chaingunners.
The final large room where the floating eye is located is the exit for this level, and is accessed via obtaining the blue key in the fenced area outside, closest to the raised platform with a wood door. To get the blue key, go through the small yellow door and up to the platform. There is a switch that is in one of the alcoves that one of the Baron's came out of. Hit it, it will lower the wood gate, then you run to jump from the platform over the fence to get the blue key before the wood fence closes. Once in the fenced area, get the blue key, and walk to the other end of the fenced area, you will be teleported back out to the open area.
Once you reach the switch-activated lift in the "sewer" area, rather than riding it up, walk through it to the other side. Here, along with a security armor and rocket launcher, there is a Baron-faced wall. Press the use key on it as you would a door or switch. Although you won't be able to hear anything, it opens the locked door near the stairway you lowered to enter the sewer area. Behind it is a pathway leading to an ammo cache and a combat armor vest.
In the "library" area in the north is a wall with two red flags on it. To open it, press the use key on the lights to either side of it. Behind it is a lift to a soul sphere.
As soon as you enter the room with the floating eye surrounded by a green symbol, turn to your left and you will see a narrow door. Shoot it to open a small room containing a megasphere.
In that same room there will be a hallway with a Medikit at the end. As soon as you get to the end of the hallway, run back and make a right. A platform will have lowered revealing a hallway with a backpack along with several rockets and clips.