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After having defeated Page's missile attempt, you're now after the man himself. When Jock drops you off here, if you hadn't already discovered the imposter mechanic at Morgan Everett's home, you'd better say goodbye to Jock.
There's a control tower nearby at #1, just to the west, with a sniper on top so beware. If you're interested in sniper ammo (and the obvious entrance into the base - this walkthrough follows the other however), head over to the tower base and the locked door. Use your picks since it's easier but there is a key in the building we're going into next, however it's fairly far away.
Before taking the ladder up, disable the LAM on the wall. Head up and take down the guard for some 30.06 ammo. Hack into the security computer terminal up there to open the blast doors (for the alternate entrance to the bunker) and disable a camera.
Climb back down and take the lower ladder, where again, there's a LAM waiting for you to disarm. Below are two crates with the precious 30.06 ammo. Now go back outside and head all the way east to the back wall, then left (north) until a small wall overlook stops you at #2. Jump onto the small wall when you won't be noticed by the patrolling robot, follow it around until you're above the overturned truck below, and jump onto it. Fall to the ground and make for the north Comm building with open door at #3. Walton Simons is inside if you decided to make a run for it back at the Ocean Lab. You can again run from him if you like. Simply Cloak and block his exit with a crate. Inside the room is a downed guard and nanokey to the tower we were just in.
Enter the small side room with locked trap door, and either pick it or try your keyring. For some reason, I had a storage access key that actually worked. Below is some supplies and an augmentation upgrade canister behind safety glass. Bypass the keypad with your multitools to get it, and then toss a LAM at the lockers if you want to replenish your multitools.
Head back out of the building and west to the hill. Climb the hill to avoid the robots, climb over the blast door and wait for the robot near Hangar 18 (map #4) to have its back to you, and sneak just inside the busted hangar doors. Inside are two MIB and an MJ12 commando. Switch on Cloak for the easiest way, or simply destroy them as you please. On the right (north) side of the hangar is a set of broken stairs. Jump onto them and move across the catwalk to the building on the west side of the hangar. Crouch and jump through the window and talk to the guard, who gives you a security logon for the blast doors, "a51" and "xx15yz". But we're not going there.
Crawl back through the window and onto the diagonal fallen girder that goes from the ground to the roof of this small building. Climb onto the roof to access some bonus points and a storage nanokey. Turn on speed (if you have it and jump to the top of the giant fan cylinder. You'll be on top of a grate with a small unlocked opening on top. Below is a giant fan. Alternatively, you can access it from below if you unlock the small door to the cylinder. Throw a LAM down toward the fan (doesn't matter where, it won't pass through) and blow it up, then jump down, down down. You fall in a pool of water with a ledge and stairway nearby.
Take the stairs and go through the corridor until you get to the security computer terminal. Hack it to disable the camera and/or turret nearby, then proceed into the next room. Hack apart the boxes on the lift, and take it down. Ahead will be a laser grid. Run through it and a small security bot will be unleashed behind you but too far to catch up. Run forward into the next room and down two sets of ladders to the ground. Congratulations, you've reached the bunker. Tong and Page both message you, and you learn that Page is in sector 4. Hit the switch to the bunker and head through one set of large doors and then another.
In the next room is a turret ahead and a camera on the left side, out of view from outside the room. Sneak behind the crates under the turret, to the right side. Walk to the edge of the platform and you'll see a cat's eye laser grid below. Toss an EMP down there to disrupt the field, and then head on down and into the next corridor. Spiders come after you if you happen to trigger it. Hold up before you get to the next room with yellow generator on the right. It will start to shake and blow up. Page will transmit to you. Head around the corner where it says Station 5, and speak with the Morgan Everett hologram who suddenly appears.
This is the first of three end game proposals. Everett wants you to join him in the Illuminati to rule the world and gives you a security code, 8946. It's now marked as a secondary goal. As you can see, you're at an intersection. Straight ahead from the previous corridor (where the laser grid was) leads to the sector 3 door directly, but in the back of a gigantic cross corridor where a couple MJ12 commandos and a few troops patrol. We're going left, which leads to the left side of the same corridor but gives us the key to sector 3 as well as an aug. upgrade and possible aug canister. Notice the trap door near the hologram, locked. It takes you very close to the sector 3 door but is also close to the troops. Take the left corridor.
Soon you'll come to a robot patrolling near a barracks door on the left. Take the robot out using your Spy Drone, EMP, LAM or preferred method, and pass up the barracks door. The next door is where you want to go, but it's guarded by a camera and gun turret. You can shoot the camera with your sniper rifle, or throw a LAM at the turret, or bypass it quickly by going around back. Your choice. Head to the door and enter the 8946 code from Everett. Turn on your cloak if you have it, enter the room with the sitting WIB and trooper, and read the datacube next to the dead body on the table. It's to Julia from Alain, and gives the code 0169.
Head back to the Barracks door and enter the 8946 code. Inside is a medbot, and on your left, a containment chamber with the dead body of Alain. Behind him is a nanokey to Sector 3 and an augmentation upgrade canister. Enter the code 0169 on the keypad and grab them. Another chamber has a Regeneration/Energy Shield AUGMENTATION CANISTER
, but requires multitools to bypass. It's also guarded by a greasel.
Head back to the hologram where Everett appeared. If you're up for a fight, take the other, south corridor and you'll face the commandos and troops. With Cloak you can simply pass them by and use the nanokey on the south wall Sector 3 door, then enter unnoticed. However, take the locked trapdoor near the hologram if you feel like taking your chances after popping up near the Sector 3 door and MJ12. If you're a sniper be sure to take care of the sniper on the small crane to the east where the troopers are and climb it for his 30.06 ammo. Head through the Sector 3 door using your nanokey when ready.
In the next room is a lift and some crates. Before you press the switch for the lift, you'll be getting a nice surprise in the form of 2 MJ12 troopers and an MIB. Hit the lift switch and hide behind the crates. When they arrive, it's your call. The troopers have an EMP grenade, so if you merely shoot them and then kill the MIB away from them so the explosion doesn't frag their bodies, you're free to the grenades. Take the lift down to sector 3 proper and another proposal waiting.