Walkthrough: Wait until the elevator has reached its destination and don't forget to wear a gas mask #1. Exit the elevator and choose a good weapon from your arsenal again #2, because you're about to take part in new battles.
You must now fight your way through a long corridor where you'll be dealing with amoeba. Remember that it should still be your top priority to keep destroying the tanks found along the way. Some of them will be on the ground #1, but you should pay more attention to neutralizing all the tanks seen on nearby walls #2. Prevent the creatures from moving in too close during this battle, because you can die easily here.
Thankfully you'll have a chance to restock during this battle. The first stash can be found after you've left the elevator #1. As for the other one, you will find in to your left in the middle of the corridor. It's going to be a red locker #2 and aside from standard ammunition you'll also have a chance to collect 30 rounds of gold ammunition.
Eventually you'll have to locate a ladder #1 and use it to leave this area. The good news is that you shouldn't be attacked by anyone else in the meantime. Proceed towards a new control room #2. You won't have to do anything here - wait until you've received updated orders.
Choose a door located to the right of your partner and press a button located on the wall #1 to open it. Head down and start moving towards a ladder seen in the distance #2. Use this ladder to get to an upper balcony and then immediately approach a second ladder.
After you've made your way to the highest balcony you'll have to make a few steps forward and press the action key to access the crane #1. Notice that you've been given a chance to control the crane and this can be done by using movement keys (WSAD by default). Keep looking at the left monitor while moving the crane. You'll have to position it above one of three blue points #2.
Wait for the icon to change its color from blue to green and then hold a mouse button to lower the crane's arm. If you've done everything correctly you're going to be rewarded with a short cut-scene #1. Follow these exact steps with two of the remaining blue steps. Once you've listened to new orders move the crane to the upper right corner #2 (two orange plates).
You may now exit the crane and if you "parked" it correctly you'll be allowed to enter a nearby balcony without having to make any jumps #1. Use this balcony and then jump down through a hole in the roof #2 to return to the control room.
You may now start following your teammate by heading inside a newly unlocked corridor #1. You'll soon find a new elevator #2 and naturally you'll have to enter it.