Meet Your Contact // Follow JB
Proceed up the alley a short ways to meet with your contact. Follow him deeper into the city, vaulting over barriers and ducking under tight-space when necessary.
Upon reaching a closed gate, JB will instruct you to take cover behind the nearby wall, marked by two blue silhouettes. Crouch behind it.
Plant First Locater Beacon
Plant the locater beacon on the control box, right next to your partner (on the right side of the courtyard). You may also want to try out your GPS now (by pressing "select" or "back") which shows a direct path along the ground to your target--this is useful for whenever you're not quite sure where to go next.
Shoot the Alarm Boxes
After planting the first beacon, wait by the gate ahead for JB to open the way. Follow him up to a second gate where you'll have to target two Alarm Boxes beyond. Ready your gun, place the reticule over the red, glowing boxes, and pull the trigger until both are destroyed.
Plant Second Locater Beacon
With the alarms destroyed, continue onward after JB opens the gate. Proceed into a parking garage and then onto an elevator, riding it to the next floor. After stepping off the elevator, you'll find three guards who have surrendered. You can do as you like with them, though you'll reap morality rewards for tying them up instead of killing them.
Climb the stairs afterward to find a couple more enemies. Luckily, the Officer is facing away, making it a trivial effort to grab him from behind, forcing his squadmate to surrender. Tie both of them up and then climb either ladder up to the roof. Once there, plant another locater beacon on either of the two control boxes while your partner handles the other.
Regroup With JB
After planting the explosive, numerous soldier will begin to flood in below. Take cover behind the railing for cover and shoot the enemies beyond. You may also want to put your partner on "Aggro-Advanlce" to draw the enemies' attention away from you.
With the area cleared, climb down to it via the ladder on the left and head for the room on the right to help your partner open a gate. Shortly thereafter, you'll be given a new order from command: Kill JD.
Escape the Rooftop
With JD long gone, clamber down the stairs and into the hallway where you'll find a door you'll have to help your partner open.
Once through the door, follow your GPS's path to a low wall on the right. Just beyond are several enemies, including a few more who'll storm from the hall ahead. Put your partner in aggro-advance to draw their attention, then pick them off from behind that wall. Once the coast is clear, proceed up the hall to find a Supply Case--these puppies can only be opened if you can dispose of any nearby guards without setting them on alert, netting you some free equipment. Open this one up, then team-up with your partner to climb the nearby wall.
Almost as soon as you pull yourself up, several guards will storm in. Take cover behind the wall next to the port-o-potty and target them from here. Push forward up the corridor, using the columns if necessary to target whatever enemies remain.
Continue down a long staircase (note: your squadmate may drop off a ledge instead--don't follow him) up to a low-wall with an orange stripe that can be used for cover. Sit tight and target the enemies both ahead and those emerging from a room on the left. Once things have calmed down, you'll want to focus on a mounted-gunner in the room on the left. To take him out, set your partner to aggro-advance to draw his attention, then when you turn blue, sneak up along the barred-windows and take him out with a head-shot from the side.
With the mounted-gunner down, enter that room and push forward to the next and seek cover behind the railing to clear out this one too. After doing so, take the stairs on the right down to the lower floor. Take cover by the low wall on the bottom floor, and be mindful of another mounted-gunner on the right. Again, you may want to set your partner to aggro-advance to draw their attention.
Once clear, follow your partner through a door on the right and help him open the gate beyond. Now around that corner are two civilians and three hostage-takers. If you can manage to capture the leader hostage, the other two will instantly surrender. To do so, you'll have to sneak up behind him by crouching and walking up to him at a moderate pace--once you're close, grab him and tie him up. As long as you didn't draw their attention beforehand, the other two will surrender without incident--tie 'em up too then save the hostages.
Continue through the door on the left leading out onto a bridge. Take cover by the low wall (adjacent to a ladder) and target the inbound enemies ahead. Now one or two of the enemies are equipped with a shield, making a frontal attack near impossible. Draw their attention away by setting your partner to aggro-advance, allowing you to target the shielded baddie when they turn away. Now follow the walkway to the right, using the walkway's railing for for cover as you target the enemies below, before working your way to the far staircase leading down to their level. Once on the ground-floor, head to the marked portion of the fence and toss your buddy over (while you can clamber over yourself, it's better to let your teammate do it, since he knows what to do).
After tossing your buddy over the fence, wait for him to open the nearby gate, to the left. As soon as he has, dash into the control room and take cover by one of the windows within, enabling you to target the attacking soldiers. We also recommend aiming taking down the rocket-launcher visible out of the right window on a building to the left asap!
Once you've thinned the herd, a cutscene will show off a big, burly bad guy entering the fray. It takes several direct shots to the noggin in order to fell this guy, but first focus on quickly taking down some of his lowly companions. Once you have, rip off the control-box's cover to your left for a make-shift shield and get ready to target the big guy when he climbs the stairs and walks alongside the left window (the one just left of the control box). Your shield should provide adequate cover, enabling you to use your pistol to shoot his head at close-range. As soon as he's down, head for the area he came from and go through the door to complete the chapter.