You will heavily need the neck snap for this misson to keep your stealth. Bring the Stun Jack and a silenced pistol as well.
When the stage begins, run out to the streets and turn left at the hill. Run up, and go west to the wall. Deploy your first sniffer and go back down, sneaking behind Jandran's bodyguard. Wait for him to stop and then kill him (use the neck break). Hide his body inside the ally (there's a doorway) and plant the second sniffer.
Run out to the streets towards the office far north. Sneak when the guard approaches the door and starts muttering the code to himself. A sniper to your east will ask you what you're doing - ignore him. He will not blow your cover unless you pull a weapon.
Enter the office - the security is disabled since you caught the code. Kill the guard here with a silenced weapon or the neck snap (otherwise hit him with the stun baton) and download the MetaGlobal records on the computer. Exit via the other door and you'll arrive at a garage. Snap the guard's neck (or use the baton) and grab the DSC-1 from the crate. Kneel and zoom on in the sniper - sift his head. Drop the sniper rifle and race north to the third viral sniffer location.
Backtrack to the garage and grab the DSC-1 again. Kneel at an angle and snipe the warehouse patrol. This will trigger Foreman Jones. You must snipe him before he sees the body - you can do this easiest when he opens the door to go outside. If you don't like the odds of a killshot, he can also be killed or rendered unconscious with Dormagen or sarin gas.
Turn towards the ledge with a platform. Crawl through it and kneel. Zoom in on your weapon to see another sniper just in front. Sift him and drop the sniper rifle. Head a bit forward and to the left. You will see a passageway - follow it and hide inside the doorway you see. A guard will approach you, then move on with his back to you. Use the Stun Jack on him and hide his body inside the door you were using.
Go towards the ladder to the west and use it. A sniper is up here too, so wait for him to turn his back to you before you grab the sniper rifle. Kill him, drop the weapon and go back to the ground level. Wait at the side of the university doorway. A guard will run out, so zap him with the Stun Jack and hide his body where it can't be found. Another guard approaches you. Stun him and leave his body. Enter the doorway and plant the last sniffer to the right wall.
You can now enter the Agency safehouse - backtrack to get your equipment. Go back to the warehouse using the vent you crawled through earlier, and enter the office. Use the DSC-1 to snipe the gate lock and open it when you hit the streets. Use the left entrance to the warehouse, then break out your guns. You can now shoot enemies, so kill the two guards inside and plant a beacon inside the truck. Use your map to search for the two containers and bug them as well.
Hide your weapons and then change into the outfit inside the locker room. You will now be incognito, so use the Stun Jack to zap everybody inside the tunnels.