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You've been diverted from Hong Kong to Hell's Kitchen again, and dropped off on the 'Ton Hotel rooftop. Descend the ladder to the fire escape and Paul's apartment window. Climb through and speak with Paul. He'll tell you about UNATCO's conspiracy, Silhouette, etc. Talk to him until he runs out of dialogue. Supposedly there's evidence in the NSF HQ to the west (through the tunnel that was blocked before), so he hands you an image of the place.
Check Paul's hidden bookcase stash as before via the painting, code 4321. Head downstairs and you might see Sandra and her Father talking once more. If you offer the father a gun, he'll shoot JoJo when he comes soon after, and Sandra will stay at home, both of them a little happier. If you refuse to offer him a gun, you can protect them once JoJo arrives and begins to threaten Sandra, by prodding JoJo unconscious, but Sandra will run away to start a new life... to Eugene, OR she says... not necessarily a bad thing IMO.
Return to the Smuggler to rebreak the mirror (see Hell's Kitchen 1) and other joints if you feel like it, as you won't have any combat for a bit and can relax. When you're ready, go through the west tunnel, which is straight ahead from the subway stairs. Follow it to the NSF HQ, where a bunch of UNATCO troops have taken over, so you're safe for now.
As you approach the building, Alex transmits you some directives. You'll need to transmit an NSF signal from the rooftop tower--apparently Alex has defected as well--but you'd have to hack the computer or go through a hatch on level 1 to a secret area in the basement of the building for the codes, which can only be accessed by a computer on level 3. It's not very complicated, even though it may be a bit confusing now. We're going to go through the hatch and get the codes... yes, the long way even though we can hack the computer, simply because there are many useful supplies and weapon mods.
Enter the HQ from the main door just around the corner once Alex sends his message. In the SE corner of level 1 is a hatch on the floor indicated by a white circle. You can only open it from the computer on level 3. Near the stairs, also on level 1 is a hazmat suit in a crate. Pick it up as it will come in handy later. There's also a repair bot you can use to recharge power.
The computer room on level 2 has an interesting conversation between two UNATCO troops. In the locked room beside it there's a datacube with the access codes to the computer we need to use on level 3. If you want to skip the biocell also in the room and just feel like hacking, head up to level 3 and into the computer room. Read the datacube which warns of halon gas. Fortunately there's a venting switch on the wall so hit it and the gas in the next room will dissipate. Use the medbot here as well for any upgrades/installations. Enter the mainframe computer room, and wind around the computers to reach a security computer terminal on the wall.
Either use the computer codes you got from level 2 or hack into it, and open the hatch on level 1. Return to level 1 and the hatch.
Climb the ladder down, go through a door, and you'll be in a room with two doors. Take the unlocked door to the right and you'll see a laser grid with matching electronic panel. Rather than wasting multitools, you're going to run through the grid, crouch and enter the vent nearby on the left side against the wall. Wait for the alarm to stop and exit, then continue through the door.
Within this room is another unlocked door and some crates. Beware the TNT crates above the wooden ones. Carefully set them down first.
Head through the door and you'll find more laser arrays and turrets. This time there are three metal crates nearby, so rather than using multitools, stack the crates two rows high but next to the lasers, hop on, save your game and jump over. Speed enhancement helps but is not required. Once on the other side, if you don't mind a bit of non-realism, pick up the crates through the laser... and restack them against the next laser array the same way, and hop over safely. Unlock the door beyond and enter into a room with a gas leak near a crate and barrels.
The locked door to the right has EMP grenades and a hazmat suit. To get at the crate in the main room you'll probably need a hazmat to avoid any health loss. Proceed through the door on the left into another corridor with lasers and electronic panels.
It's possible here to not waste any multitools (in fact gaining two) while taking minimal damage. Ahead of the first set of lasers is a niche on the left. Run through the first set and into the niche, where a set of ballistic armor is handily laying on the ground along with a box and crate. Wait for the alarm to stop.
Enter the corridor again and jump onto the metal crates stacked up just before the next set of lasers. Ahead on the right you see some gas with box and crates. Move to the left just before the laser and shoot boxes and crates with your pistol to break them. Inside are two multitools. Equip your ballistic armor, run through the first set of lasers, quickly kneel down to take the multitools, and run around the corner into the next computer room, safe from the turrets. It's likely you took a little bit of damage, even with the armor on, but nothing the medbot in the level 2 computer room cannot fix up!
Break the glass on each side of the case in the room with two pistol shots apiece, and take its contents. Open the locked door inside the room to enter another computer room with a case. On the top of the case is a datacube, so read it for the access codes to the rooftop computer: "mcollins" and "revolution", and "napoleon" and "revolution". Two of them with the same password. Head out and up the stairs in the other room to the outside. If only you could have through this door from
the outside... it would have been so easy! But alas. Now head to the medbot on level 2 if you desire, and then to the rooftop via the stairs.
Enter the satellite control room on the roof, pick up the LAM on the floor and either hack the computer (why bother now?) or enter the code you recently received from the basement: "mcollins" and password "revolution". Press all the buttons in order to align the satellite and open the nearby door.
Proceed through the door, and login to the computer using the "napoleon" and "revolution" username and password. Once you broadcast the message, get ready because the UNATCO troops are about to have your name on their bullets, courtesy of a Walter Simons. It's time to escape.
By far the easiest way is to activate your speed augmentation, hopefully upgraded by now, and simply JUMP off the east edge of the rooftop to the street below and run, taking minimal damage and hightailing it back to Paul's apartment with nary a UNATCO uniform to deal with. However, if you don't have that option, you'll have to go it the hard way, down the stairs with lots of UNATCO to fight or run by. In the end, your goal is to exit the area and proceed back to Paul in his apartment via the fire escape.
After you exit the tunnel, take an immediate right, then left down the hotel back alley and jump up onto the fire escape. Before you step into his apartment however, heal up if you need to because you may be fighting soon, it will be your choice.
When you enter, Paul will be sitting down and talk to you about Walter Simons being part of an organization called Majestic 12. Men in Black will then come knocking on the apartment front door and order you to disarm. Here's the choice. If you want Paul to survive, do not
follow his advice and exit through the window, saving yourself. If you do that, upon exiting through the subway station back in Battery Park, you'll be informed of Paul's death.
Instead, if you still have the assault rifle and a lot of ammo, you might consider fighting along side Paul against the mighty Men in Black when they crash through the front door guns ablaze. Each time one of them dies they explode so it's very possible and not difficult to die without a lot of firepower.
Paul is in fact immune to their fire so letting him advance on the Men in Black and UNATCO is preferable and then joining in as support. Hiding behind one of the chairs and firing from a distance is handy until the chair blows up, and even then stay back as necessary until it's all clear. Eventually you both will win as long as you stay alive.
The other choice is to hide in the closet until the fighting stops and only Paul remains. That way you don't get damaged and Paul survives.
Whatever you decide, when the battle is over, head through the apartment front door and Paul will follow, saying to find Jock in Battery park. He gives you the subway access code 6282. Walk toward the stairway down and Paul will scoot ahead of you and begin another battle with the UNATCO below. Wait until it's over or join in, your choice. There are a lot of UNATCO down there and it's a good opportunity to loot their bodies for more ammo. After you've cleared below (or before if you don't wish to wait for the battle), turn on some ballistic protection if you have it, and also your speed augmentation, and make a run through the front door, avoiding any remaining UNATCO, take a left, and sprint toward the subway station stairway.
Descend the stairs, enter the code 6282 on the panel, and make your way to the subway. Take it to Battery Park and exit the stairway. There is no way to avoid being captured by Gunther who's waiting on top. If you stay and fight him, you will die... since he's invincible. I tried my best at sniping him my first game, using all my ammuntion at shots to the head, but he would not go down. You'll be taken to the Majestic 12 facility as a prisoner and stripped of all your belongings. Don't worry, there's hope.