Head over to the small security cabin on the far end of the area and hack the PC to shut down the camera (and robots, if you can). Don’t open the door; this only alerts the guards, and you wouldn’t want that.
On the left side of the manhole you entered is a large container. Use Jump Enhancement to hop onto it and from here, tranquilize the guard up ahead, then hop over [750XP]. Moving slightly to the left - while still on top of the crates - allows you to spot a Heavy guard in the distance down below. Wait for him to back away (since there’s a camera nearby), then tranquilize hem and wait for him to fall.
The next guard you’ll want to tranquilize is the sniper on top of the crates with a large “2” printed on them; a ladder leads to him. When he’s downed, enter the building he’s standing on. You can do this either by destroying the breakable wall on the left of the building, using one of the windows (cloak helps here), or via the door; the guard inside is sleeping. The locker contains [TONGS EXPLOSIVE PACKAGE], [1000XP], [GHOST 500XP], [SMOOTH OPERATOR 250XP].
If you can tranquilize the sniper on the roof at the building on the far end of the sea port, all the better. Otherwise sneak over to the ladder (with a little help from your cloak aug, if you wish), but beware of the camera. Climb the two ladders and down the sniper if you haven’t already done so, then go inside the building.
Head through the doors until you reach the main hall. Snipe the Heavy guard on patrol, then move over to the nearby stairs. Wait for them to finish their conversation and start taking them out. The first you should down is the one almost below you. When the other two have been sniped, continue onward.
Move to the security booth to the far northwest side and hide behind the window. Wait for the guard to come out of the room and take him down, then go in for the second takedown. The PC here can shut down a camera and turret.
All that’s left for you to do now is to head upstairs, take down the two guards, go through the door, and place Tong’s package [1000XP, [GHOST 500XP], [SMOOTH OPERATOR 250XP].
As the cutscene plays, Tracer Tong (yes, from the original Deus Ex, but 25 years younger) also makes his escape with “The Tracer” boat.