A lot of people feel there's only a handful of ways to beat the flagship. The most popular method is to kill the crew except for the guy at the laser auxiliary weapon. But there are several good ways to beat the flagship, and they work best if you start planning ahead for them very early into your game. By sector 3 or 4 you should already be identifying your strengths against the flagship and deciding which strategies are going to work best for you.
I'll admit that the killing crew strategy is highly effective, and you can reliably get both a cloak and crew teleporter if you put yourself to it. But there are other perfectly good ways to win, even if you never neuter the flagship during the fight. All you really need to do is reduce its hull hit points to zero. Don't forget that.
METHODS TO WIN:
1.) Guns--The simplest and most straightforward way is to use powerful weapons. Double burst laser III, burst laser III plus halberd/glaive beam, flak plus beam, breach missile plus hull laser, all of these are good choices. You want to get a weapon setup that can reliably get rid of the shields and also deal high damage. This usually involves using a combination of weapons, because the best damage dealers aren't the best for getting rid of shields and vice versa. Flak are the exception, they are both good at getting past shields AND good at dealing hull damage (best vs flagship because it's so big) so flak are particularly good against the flagship.
Strategy: once you have good weapons, just let them charge and get a good volley. Bring down the shields, hit the weapons or cloak second, and try to keep important systems down while you blast away at the hull. A hull laser II may seem weak most of the time, but it'll do 6 damage in a volley if it hits an empty room. Cloak is especially great for defense if your weaponry is slow-charging, because you'll have more difficulty holding multiple systems down. You can also mix in combat drones to help keep other systems down while you hold shields down with your weapons.
2.) Boarding--this is widely considered the best way to beat it, but it doesn't work as well on hard difficulty. You need at least 2 good boarding crew but it's best with 4. I actually don't recommend this strategy for newer players because it's too easy to lose your boarding crew due to an accident. It's especially tricky if you have only a 1x2 teleporter. But done right it can work very well. You can also mesh this strategy along with others. You'll want crew teleporter to 3 (2 is acceptable if you have 2x2 OR if you only intend to hold down auxiliary weapons).
Strategy: Beam two units to the missile weapon and start taking it down. As soon as teleporter is ready again, beam two over to either the beam or ion weapon. Once it's ready again, pull back the two in missile room, next send them to the third weapon. IMPORTANT: Do not send anyone to the laser room if you intend to kill the rest of the crew. On hard, you might just kill them all and hold a team inside to jump back and forth between missile and shields, since the two center weapons are connected to the rest of the ship. Once you have it down to only the laser, you should be fully safe. Then you have to figure out a way to get your crew into the main section and kill off the rebel soldiers. The most important thing here is to take out their medbay and hold it down. A fast-charging crew teleporter can help you get two waves of two crew inside before you have to pull them back-reconstructive teleport also saves you time. Second phase is a bit more dangerous but you want to take down the missile first and possibly drone control second, or maybe beam weapon second, depending on your defenses. Third phase is tougher because you have to break down the super shield, so get in there and take that missile weapon offline as soon as possible, and pound that ship up as fast as you can if you can't defend yourself against the power surge. Go ahead and blow it up with your crew on board, you win anyway. Don't sacrifice your game just to save your boarding party.
3.) Missiles/Bombs--You can use missiles or bombs to knock down and hold down the ship's systems while you work on taking down the hull with whatever else you have. You can save up missiles for the end by holding your missile or bomb weapons in cargo for your final sectors and swapping them into weapon slots when you fight the flagship. The breach missile is great for taking out any auxiliary weapon in one hit and can also do a number to the drone control in phase 2. Ion bomb costs only 1 power yet it can incapacitate a system for a pretty long time. You can use one ion bomb to take out the shields and hold them down by stacking up the ion damage. Ion bomb also deals 8 damage to the super shield (tested!). If your weapons crew is well trained and you don't miss, you can hit again in under 20 seconds. The breach or fire bomb are a pretty good way to take out the med bay if you plan to send in crew, fire bomb especially if you're using rockmen. Taking out the medbay is also good just to make sure they can't heal up. Some of the crew may be killed just by your laser attacks, and that'll weaken their ability to repair the ship. If you can get it down to 1 crew, even if you aren't boring the ship, that'll still make it far easier to take the ship apart. If you use a missile, you'll want at least 2 missiles or a pegasus or swarm missile. Fire the weakest missile first, then fire progressively stronger missiles slightly later. The defense drone will fire at the first missile and let the others pass (usually). If you do a bit of damage to the drone system, the defense drone might go offline.
4.) Defenses--There's more than one way to survive the attacks the ship throws at you. You'll want some kind of good defense to survive. A good attack may be all you need, but it's best to combine attack and defense. Max shields and high evasion are great, but alone they are not enough. Cloaking can help give you a big edge. Defense drones can really help keep those pesky missiles, boarding drones, and hacking drones out.
Strategies: If you use one power bar of cloak early enough in the power surge, you can often have it cooled down by the next power surge. Learn to time it, don't just pump three power bars in unnecessarily. One defense drone is good, but two is great. Two will shoot down the missiles so well you might not even need to worry about taking out the missile system. Two can much more reliably shoot down the hacking or boarding drone, which is great because if you get the ship to use up 10 drone parts, it runs out for that phase! Anti-drone drone is great on second phase because it'll take out the attack drones, and the flagship also pays drone parts for those.
5.) Hacking and Mind Control--I'm lumping these together because individually they are pretty simple. They are an offensive system that you can use to shut down the flagship's attack (hacking) or defense (both).
Strategies: Mind control is pretty simple. If you have it up to three bars, you can reliably have the crew kill each other with the mind control until there's only a few left, and it won't involve taking out the medbay! Easy! Hacking can be used in a number of ways. If you hack their shields, it can make up for a mediocre weapon setup, enabling you to better get shots on target. If you hack their medbay, you can use it to kill them once you convince them to run in (works best with crystal lockdown), or just take advantage of the time it takes them to open the door and kill them in the adjacent room! If you hack the drone system on phase two, you can initiate the hacking pulse during the power surge, to balance out the incoming DPS. To get past the defense drone, you should use a missile to distract it, then send your hacking drone right behind it. Or you can shoot out the drone system first, then hack the flagship while the drone system is down. Even if they repair the drone system, your hacking drone stays in place. Just choose wisely where you put it. One advantage to getting hacking is if your plans get changed before you enter battle with the flagship, you can formulate a new plan and choose a different room to hack in order to facilitate the new plan. It gives you flexibility.
6.) Screw the crew--Some plans involve keeping crew alive so the ship can't repair itself. But if you can take important systems (or the hull) down fast enough, who cares? Take out the main guns and butcher the crew in the first phase, then you can board the ship in phase 2 and 3 and run around all you like. If you have enough boarding party, you can hold down multiple system while your shots beat the hull to a pulp. Or with several fast-firing weapons, you can hold down the systems without crew. A halberd beam can hold down 2-3 adjacent systems even while the AI is repairing them. If you spread fire around the ship, like with a fire beam, you can take out the crew WHILE holding down the systems. A fire bomb isn't enough by itself, but a fire beam is if you can keep shields down for it, and a fire bomb plus beam are amazing together! Also, any breach weapon can hold a system down after the AI has taken over.
6.1) Breaches--You can kill the crew and still hold systems down if you put hull breaches in those rooms. Breach missile and breach bomb II are powerful enough for general use, but even a breach bomb I works great if all you want to do is get a breach. Breach bomb I sucks with tons of crew to repair, but once the ship is on AI, breach bomb I is Chuck Norris. You can also get breaches with other weapons. Hull lasers, hull missile, heavy lasers, and crystal weapons all have pretty good breach chance. Just because it's a hull laser doesn't mean you're wasting shots hitting the missile weapon. (But once the HP is low, consider hitting an empty room.) I don't normally suggest using hull weapons, but they mesh well with a breach setup and also with a high damage setup (as per strategy 1).
7.) Artillery Beam--this may not be the best suggestion but it works. If you mix enough defenses (shields, evasion, cloak, defense drones for instance), you can focus on micromanaging your defense while the artillery beam charges. Upgraded door system and engi crew can keep the ship together, you can pretty much ignore the boarding drone sometimes, or blow it up until the flagship runs out of drone parts. That artillery beam can charge in 20 seconds at max level and will deal around 4-6 damage per hit, fully shield piercing. Slap an ion weapon in the weapon slots to take out that super shield, and it's actually not that difficult to take out the flagship this way. One advantage to it is all the power bars you save by not spending them all on weapons. You can apply them to maxing out engine power, for instance. The difference between 45% evasion and 55% evasion might be bigger than you think it is.
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