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I'm at the part where you have to defend the flagship against waves of attacking zeppelins carrying hordes of soldiers. I'm playing on Hard difficulty, so enemies soak up enough damage that I can't quite keep up with them, and they slowly destroy the ship's core. (I don't even want to think about dealing with this on 1999 Mode...)

What strategies are effective in this fight? Should I be saving my "air strikes" for the gunships, or should I be using them against the infantry on the decks? How do I deal with the Patriots?

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The Washingtons are the Columbians, while the Vox Patriots are actually Lincolns. TMYK –  Mondrianaire Mar 31 '13 at 20:22
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This one took me a few times as well. Ultimately, you want to prioritize:

  • Gunships (which cause a medium airstrike cooldown)
  • Patriots on deck (which cause a low airstrike cooldown)
  • Zeppelins (which cause a high airstrike cooldown)

Gunships (the boats that fire rockets constantly) will do the most damage to your airship core and need to be dropped first.

Zeppelins don't actually directly damage the airship core... they just launch Patriots. If there are no gunships to target, you can use a short 'airstrike' cooldown to help you clear the deck, then take down any Zeppelin's that are targetable with the next 'airstrike'.

Also remember that, when dealing with Patriots:

  • Clear as many of the humans off the deck as you can first. You'll want to damage the Patriots from behind and that is hard if you have the Vox pumping you full of lead.
  • If you've taken Possession upgrade, it's usually better to CC one of the humans that toss fire grenades or fire rockets. They'll do some damage to the Patriots, then helpfully remove themselves from the fight.
  • Patriots can be briefly controlled with Possession, but will become hostile afterward. Since they come in pairs, alternate which one you crowd-control (CC), get behind the hostile one while it's distracted, and fire into its back for bonus damage. If you alternate, one of them will die and the other one will be low enough that a few shots with a higher-powered weapon should drop it.

In addition, there are RPGs on the wall beside the starboard (right) side of the core and another one on the deck below. These do decent damage (especially if upgraded), and Elizabeth should feed you enough ammo to keep you firing them. If you haven't upgraded the RPG, though, favor another heavy-hitter that you've upgraded (in my case, it was the Hand Cannon).

Lastly, the enemies all come in waves triggered by clearing the last one. You can use this to your advantage by leaving one low-damage person alive, kiting them around (or just letting them fire at the core and do negligible damage), waiting for your 'airstrike' to come off of cooldown, then finishing the straggler off. This will make sure you have an airstrike ready for the beginning of the next wave.

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Point-blank sniper rifle right in the back took them out in about 6 shots on hard. –  Sterno Mar 30 '13 at 20:27
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To add to this: "leaving one low-damage person alive" - using possession on a patriot seems to reset their AI - once it wears off they will attempt to attack you, and not the core. What I did was possess a Patriot and then use the sky-line to get to the Crow's Nest at the touch - he can't get you up there, and this gives Songbird time to recharge and allow your shields to come back up. This let me take out the last couple zeppelins I needed, and zip down to take pot-shots. –  Gauzy Mar 30 '13 at 20:40
    
Also, by this time you should have accrued quite a bit of Gear. There are a few that allow for 'Brief Invincibility' that allow you to ignore all other fights and completely concentrate on the Patriots. Playing through this on 1999, I found that equipping gear that maximized air-rail benefits was the best way to go, as the rails are available literally everywhere on deck. –  Mondrianaire Mar 31 '13 at 20:26
    
"enemies all come in waves triggered by clearing the last one ... leaving one low-damage person alive" - This doesn't seem to work anymore? I just tried this, and I continued to get more waves anyways. –  BlueRaja - Danny Pflughoeft Apr 11 '13 at 9:12
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I just finished the game on 1999 mode, and my complete guide to the difficulty level is here, but I'll summarize my strategy for the final fight:

Setup

My weapons were the Repeater and the Crank Gun. Both of these are plentiful where the enemies are, and that's where you're going to be. I never had to worry about ammo, as whenever I killed an enemy, I was getting more.

For gear, the critical bits were Brittle Skinned and Winter Shield.

From the generator area, if you face the window you jumped down from to get in, you'll see on the left is a rack of RPGs, with a crate of health and salt restoratives under it. On the opposite side is a rack of carbines and sniper rifles. In the middle is a few vigors that you probably already have, which you can take for free salt. Behind the middle console is a tear you can open for more health kits.

Down each of the sides of the upper deck from the generator are a couple of cover areas that both have a salt and health kit each.

The Battle

Songbird

You only win when the zeppelins have been defeated. The enemies will continue to spawn until you do so. Therefore, prioritize the zeppelins if you can. Sadly, these take the longest to down, and Songbird will be out of commission for a while if you ask for one to be attacked.

The rocket gunships have terrible aim. I let one stay at the end of the ship, shooting like crazy, and it barely scratched my core. It did hit me a few times though, which was a bummer.

Clearing the bridge is good for times when you're just being overwhelmed and your next target is a zeppelin.

Combat

You've got three types of enemies to worry about:

  • Unarmored humans with repeaters
  • Armored humans with RPGs
  • Patriots

When a group spawns at the end of the ship, jump on the skyline and do a skyline strike on one of the unarmored humans. Then, unload your repeater (or whatever weapon you have) into him. Pick up his repeater, and off the rest of the unarmored humans. If you have Winter Shield, it should last you through the encounter with the humans. If not, you can use Charge with the invulnerability upgrade to restore your shields and give you a few seconds to recover/reload.

Meanwhile, the Patriots are making slow progress across the ship. You can Charge into them, or just whack them with the skyhook if you wish to engage the Brittle Skinned damage bonus. Then, unload with the repeater, or a crank gun if you have one already. In a pinch, you can use the RPG, but the small clip and long reload delay mean your DPS is going to be relatively low.

Once they go down, make sure no RPG guys have dropped near the core. If they have, Undertow them off the airship. If they're in close to the core, you might have to knock them down off the upper level, and then again to knock them over the railing.

As long as you don't let the RPG guys get in close and stay there, and you don't just completely ignore the Patriots, the core won't take that much damage.

At this point, you can restock health or salts, and regroup for the next wave. Target Songbird on a zeppelin if you haven't already.

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RE: "The rocket gunships have terrible aim.", I experienced different behavior, and I wasn't in 1999 mode. If I left one up while I cleared the rest of that wave, my core took a quarter of its full hit-points at a minimum. If I left it up for two full waves, the core had taken enough damage that Patriot damage was a serious threat rather than a passing annoyance. Maybe I was clearing waves more slowly, but I don't think it was taking me longer than a minute or so to clear the deck each time. –  Shaun Apr 8 '13 at 21:09
    
@Shaun, I left one up for several minutes and it just shot rockets at random locations around the bridge. If they're causing a problem, by all means remove them. I just didn't find that to be the case. –  agent86 Apr 8 '13 at 21:32
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