This is a quick guide to beating the flagship on hard mode in FTL. I'll try to keep it brief since I don't like to read overly long guides myself. This guide assumes that you know how to play FTL and know the basics and can beat the game on easy or normal, but are struggling with hard mode.
Introduction and General Tips
The goal of FTL is beating the flagship, and your entire run up to the final battle should be about preparing your ship for this task. The following are the only realistic strategies for doing this, with a few marginal ones that I include for fun:
True for all strategies:
- Try to get 4 shield pips and at least 45% evade (with a trained crew). 3 shield pips or less evade is feasible if you have a cloak, but not both at the same time. Crazy low-defense, or even no-shield runs are possible but not realistic.
- Always try to get hacking, and always use the hacking drone on the FS' shield room. The one exception to this rule may be if you are using bombs, to drop the FS' evasion to 0 to get guaranteed hits, but even then the shield room is almost certainly the better choice due to its position in the ship, blocking access to several other rooms. Think of hacking as a universal key that is helpful in any situation.
- Cloak is great, use it to get by the missile volleys and the special attacks on phase 2 and 3, especially 3 where you should save it for that.
- Sell useless augments in the final store you find: zoltan shield, long ranged scanners, scrap/drone recovery arms are all great augments for your run but are useless against the flagship. Sell them and buy weapons, shields and evade.
- Missiles are worthless. Sell them.
- On phase 3, you can abduct the FS' boarding teams by letting them board, jumping away and dealing with them in peace.
- Exploit the hacking drone trick on phase 2: launch the drone, wait for the defense drone to fire its shot at it and immediately pause and depower the hacking drone, wait a second in real time and then repower, this should dodge the defense drone's shot.
The Gunship Strat
The Gunship strat
This is simple, get as many lasers or other weapons that can penetrate the FS' shields and then damage it. Some guns are more efficient than others, the Burst Laser II is the best, Flak I and II are good for penetrating shields before launching a targeted volley. A few of the ion weapons are okay, but I avoid ion myself.
A good rule of thumb for all the guns is: it should charge as fast as possible, and offer as many shots as possible for as little power as possible. Heavy Laser I, for example, offers a single shot for 1 power, which does double damage and charges very fast, it is therefore a good weapon.
A gunship strategy can be supplemented with bombs and beams, but you should never use missiles unless you have absolutely no choice. Most beams suck because they either take too long to charge or are unable to do a lot of targeted damage to a single system. Since the best way to kill the FS is to knock out the missile room, this is suboptimal, but workable.
Overall, in a gunship strategy, you will hack the shield room, cloak through the first missile volley (except on phase 3, where you save your cloak for the power overcharge attack), activate the hack, then focus all your fire as quickly as possible on the missile room to knock it out before the second volley. With the missile room down, taking down the ship in all 3 phases shouldn't be too hard. Don't let them repair it.
Systems you will want: Hacking, cloak, perhaps Mind Control.
The Boarding Strat
The Boarding Strat
The alternative to the gunship strategy. Most other hard strategy guides recommend the gunship route, but I actually prefer boarding. The reason is that a boarding setup lets you gather more scrap during your run, giving you a wider margin for error, and well-managed boarding can get you out of all sorts of situations. Another advantage is that boarding lets you take out a significant number of the FS' crew before the final phase. The gunship strat's main weakness is that you often don't get a lot of scrap, forcing more tough decisions and lower defenses in the end. On the other hand, the boarding strat usually takes a bit longer and is more difficult to pul off well.
There are a few varieties of this strategy, depending on which boarders you use: mantis, rock or lanius. Mantis are the most common, but I find Lanius boarders to be the strongest and most versatile due to their O2 drain. Rockmen synergize with fire bombs, Lanius with breach bombs. The most important thing to note is that whichever boarders you choose to use, a boarding strategy pretty much requires hacking to lock the doors. In the case of the FS, you should first hack the shield room, then use any weapons you have on the missile room (bombs, shots) and then drop your boarders in the missile room. Your boarders will make the missile man retreat, but help will come running soon. They should be able to destroy the missile room before the second volley. A cloak, as always, is helpful to buy time for your boarders to do their work. Once the missile room is secure, drop in more boarders and use your weapons to target the door room, cloaking room and medbay. Now, start killing the crew. Leave a single crewman alive and then use your conventional weapons to destroy the phase 1 ship. The boarding strategy makes for a longer phase 1, but phases 2 and 3 should be easier due to the lack of repairs and opposition from the crew.
I did not cover Crystalmen in this section, but they are very strong too. Use their special ability to lock the doors and give them time to destroy a system.
Systems you will want: hacking (absolutely necessary), cloak, mind control again can help to distract the crew and drop evade for your weapons.
Marginal and Suboptimal Strats
The following are strategies that can work, but are either hard to achieve or very risky. I'm including them for fun, since they can definitely be pulled off and I do sometimes use them or find myself in a situation where they become my best option for finishing a run. These should be done either for amusement or as a last resort only, and are not guaranteed to lead to victory.
Fire Bomb Strat
This strategy is a little odd, very difficult and has a lower chance of success than boarding or gunning, but I'm including it anyway since it's a very fun way to complete the game and when done well, can have good results. For the fire bomb strat, you will need to find at least two fire bomb weapons, but more = better. On top of this, you will need the explosive replicator augment and hacking (to get you through your run and to seal the shield room) or, alternatively, a rockman boarding pair and a teleporter. Mind control is also highly recommended to drop evade. I don't often find myself in a situation where I can find all of these things at once, which is the reason this is not a very advisable strategy, but once you get geared up and find yourself at the FS you have your work cut out for you. Since bombs ignore shields, you don't need as many conventional weapons, though you will still need a few lasers to deal with autoscouts and other things. Once you reach the FS with the required weaponry, hack the shield room, mind control the pilot and drop firebombs in the missile room. If you've done it right, they should have a 100% chance of hitting, and if you have two of them, the combination should immediately cause the missile man to retreat. The system will quickly burn out and the fire will spread. Simply keep throwing fire bombs at different areas of the ship.
This all sounds hard but it comes down to this: if you can set fire to the missile room, and either have two rockman in that room or have hacked the shield room, the FS will eventually burn out completely. If you can get to this point, you will probably win. One hurdle to victory is phase 3's zoltan shield, so make sure you have a little bit of conventional weapons ready to bring it down (in combination with bombs) or have a zoltan shield bypass augment. However, the repair AI is helpless against fire, so once it's down you won't have much of a problem. Systems you will want: hacking, mind control, possibly teleport or cloak.
The Breach Bomb Strat
This is much the same as the fire bomb strat, but with breach bombs (and possibly Lanius). Breach bombs have one strong advantage over fire bombs: ship AI's can't repair breaches, so breaching an autoscout's or the empty FS' weapon room effectively "castrates" it, making the system permanently inoperable. The whole thing works just like the fire bomb strat, so get hacking and maybe a cloak or mind control or a zoltan shield bypass, but definitely get an explosive replicator. Lanius take the role of rockmen. Systems you will want: same as above.
The Ridiculously Overpowered Weapon Strat
As I've said earlier, a conventional gunship run should include fast charging, efficient and targeted weapons, but sometimes the game will throw you one of the big overpowered weapons (or in the case of the Stealth B, you start with one), the Glaive Beam and the Vulcan. Of these, the Glaive Beam is the best, since it lets you cut down most of the earlier ships on your run and gather a lot of scrap. Usually, after sector 4 or so, I then sell it to buy some faster weapons, but the Glaive Beam still works well on the FS. The Vulcan has the potential to take down any ship, including the FS, with its rapid fire as long as you give it enough time to spin up. For both of these, you will need to buy time to get them charged, so get a cloak and several extra points of weapons power as a "buffer" in case your weapons room gets hit and to fit extra weapons. The Small Bomb is a great complement to the GB or the Vulcan, since it's fast, bypasses shields and buys you time. Most importantly, always put the GB or Vulcan in the first weapon slot from the left, so that, if your weapons room is damaged, the big weapon will probably keep charging.
If you are planning on using a Vulcan, consider getting multiple weapon charge augments (they stack), and drone control instead of hacking, since the Vulcan, once spun up, benefits relatively little from hacking and the drone control can offer extra defense.
Finally, I will give a quick rundown of all the systems you can buy and how they figure into the flagship.
Arguably the most useful of them all, it can be used in nearly every fight during your run. For the final battle, always hack the shield room. Always leave 1 power in hacking, even if you're not using it at the moment, because it will keep the doors to the shield room sealed, which hinders the crew considerably. Obviously, you can hack the shields to easily damage the flagship. I've experimented with hacking other rooms, but hacking shields is really the obvious choice on all phases. Hacking is the most important system to get, and I always try to get it. It's not even very expensive.
The FS itself also uses a hacking module in phase 1. Should this module land on your shields or weapons room (or, arguably, piloting or engines), jump away and reset the fight. If it lands anywhere else (doors, sensors, battery, medbay), you are good to go. NEVER leave a crewmember standing in the medbay before you start phase 1, as the hacking drone can hit the medbay, activate and immediately drain that crewmember's health, killing him.
The other big one, cloak lets you outright dodge even the worst attacks if you activate it just as the enemy launches its weapons. Use it to dodge the missile volleys on phases 1 and 2, and the special attacks on phases 2 and 3. It can give you a breather, allowing for healing, repairs, repressurizing and putting out fires. Its only drawback is its cost. Phase 1 has a cloak, be mindful of it so you don't waste your volleys on a cloaking flagship.
If I decide to buy a teleporter, my strategy shifts entirely to boarding. For this, you need at least 2 good boarders of appropriate alien races: mantis, rock, lanius or crystal. Humans and slugs are fine too, but aren't optimal. Don't buy it if you only have engi and zoltan. Getting it early allows you to snowball a lot of scrap in your run, and a good boarding team is extremely useful in the final fight. Always put your first pair of boarders in the missile room, if you have more than 2 boarders the next team should go to either shields or on phase 3, to mind control.
This system is a bit underrated, and most guides advise against it. However, if you find yourself using bombs and boarders, it has great synergy with that. On the FS, mind control the pilot just as you launch your bombs to get some guaranteed hits. The victim will also help fight the crew. You don't need to put much power into this, even 1 is enough to get your volley through. Mind Control's drawback is that it's useless against autoscouts and that makes it less good compared to hacking or teleportation. Phase 3 has a mind control, try to control your mind controlled crewman by venting rooms they're in (wait until just before they've destroyed a system to buy time). Overall this is not such a big deal, though.
This is the one that I almost never pick. While having a defense drone I is very helpful during your run to the flagship, it doesn't offer much value during the final fight. A defense drone I can destroy a single missile out of 3, which is okay but doesn't offer a huge benefit. Having double defense drones may just cause them to target a single missile, still letting through 2 out of 3 (though I admit I haven't tested this much). The hull repair drone is very useful but rare and rather expensive, and often not necessary with careful play. Combat drones lack focused fire, making them almost useless on the flagship. The shield drone has interesting synergy with zoltan shields and cloak, but ultimately isn't worth it on the final fight (though I have won the game using Stealth C and its low-power version).
Medbay or Clone bay?
It's generally not worth the 50 scrap that it costs to switch out your medbay for a clone bay, although ont he whole, the clone bay is definitely better.