This mission is particularly longer, so know beforehand. After the sequence where you kill the Ceph, you will come across a large area and a Buggy so you can drive across the landscape. After you fight off several CELL on the Brooklyn Bridge and view the cutscene, you'll emerge on a new structure. There should be several crates holding ammo, grenades, and arrows. On the way down back to the ground, there are two hackable crates and a nanosuit upgrade module. Grab the Typhoon from one of the crates. When you get back to low ground, tag the enemies ahead.
Use the JAW in the crate next to the Buggy to destroy the helicopter, and snipe the rest of the soldiers. Up ahead, you’ll drive through a tube and reach a dead end. There’s a gauss sabot sniper rifle in the box to your right; pick it up. Take the zipline to your left down. Move ahead on the left side, come to a wide ditch and kill the Ceph Scorcher and Heavy. Move ahead, and drive the APC to another pipe. Move through the pipe until you reach the top of the CELL facility. Once you’re here, be sure to tag every single enemy you can see with your visor. If you’re the stealthier type, then just use cloak to jump down, crouch into a floor vent, and traverse your way through an averted fight.
Once you reach the critical area, use cloak and hack the turret to save time and headaches. There’s more Typhoon ammo in an orange crate. Destroy the black pipe and head over to your next location across the rails. DO NOT jump down and fight the CELL troops. If you have trouble finding the green console next to the stairs, use your visor to tag it. Use the console to retract the walkway. Once you reach the end of the walkway, kill the few troopers, and gain access to the elevator. Mission complete.