Go downstairs and get to a pile of dead bodies. Watch cut-scene. Now it's time for a series of Quick Time Events. Run away from boss, press proper key and get onto the bridge.
Go along the corridor and watch the buttons' icon appearing on the screen very carefully. Boss will attack unexpectedly and thanks to the icons you will be able to avoid being hurt. Search the drawers situated in the room on the left and collect ammunition and Chalice (Gold).
Reach the stairs and go up. There is Green Herb and the second Chalice Gold in the room on left. When you approach the bodies, they will get up and you will have to deal with a group of enemies. Open the door on the right and enter the control room. Read few documents and check the door in the corner of the room.
You need Bridge Keycard to open it. You will find it at the end of the corridor.
Go back to the closed door and go upstairs. Collect ammunition scattered over the location and go through the door marked on the map. Destroy the boxes on the right and go through a gate. Now you have to defeat boss.
Boss looks dangerous but the fight itself won't be difficult. It takes from 10 to 20 minutes. First of all you can put aside all your arsenal and focus on a special weapon hanging on the wall. Use a card which you have just found and take it in your hands. It works similar to a sniper gun but it doesn't shoot - it focuses a laser beam in one point. You just have to direct it on the sign Lock on and shoot. Boss's weak point are very visible.
Go up the ladder to the top. The biggest part of the fight will take place here. Loading your gun takes a while so try avoid boss's attacks by pressing proper keys. You eliminate black organisms spitted by the boss by using regular weapon (its your partner's task). When the gun is loaded, attack again. Aim carefully at glowing bulbs and wait patiently until the boss dies.