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If you can kill interior Flagship crew in phases 1 and 2, they won't be there to board you in phase 3. The most straightforward way, without AE, is to use the Crew Teleporter board on phase 1 and make your kills. Leave the crew in the Laser Artillery alive so that Flagship doesn't go into AI mode.
I have a few other ways of doing it without boarding, but they depend a lot on AE systems, Hacking and Mind Control.
If you don't have to deal with the Flagship boarders on phase 3, that makes it a whole lot easier to stay focused on the remaining dangers.
The real challenge of FTL is learning the game and how to deal with the random situations that occur. The good news is the flagship has the same three stages regardless of difficulty or randomness in the rest of the game. Thus formulating a plan works. Also keep the plan flexible.
So, to summarize, these are the things that need to be prepared for regarding the flagship. A multi-missile launcher for all three stages, a hack drone for the first stage, drone swarms and a boarding drone in the second stage, and mind control, zoltan shield, boarders (if any are left), and a surge strike for the third stage. Prepare for those in any way seen fit and wins can happen consistently.
The next biggest threat after this is missiles in general. In round 1, the one bar of cloaking will grant some reprieve. The best counter for missiles is a boarding party in the missile compartment. Take out the enemy in round 1, this gets easier in round 2&3 barring the super shield.
Here's my drone formulation (2 slots)
Round 1: Defense i + (Defense I or Defense II) , One Defense II has more utility throughout.
Round 2: Anti-Drone + (Defense I or Defense II)
Round 3: Defense i + (Defense I or Defense II)
I like mixing Defense I and Defense II because their behavior is slightly different it seems if one misses, the other may not repeat the miss.
You need:
- Transporter
- Cloak
- Hacking
Start by teleporting your Mantis or whatever into the missile room. Send your hacking drone to the shields. Drain the shields and fire all your weapons on the beam room. If you're lucky, you will not only disable the beam weapon, but also kill the guy in the room. Dodge the missile volley with your cloak.
Once your Mantis have killed the missile guy, teleport them back and send them to finish of the beam guy, if he is not dead yet. Otherwise send them kill the ion guy. Leave the laser guy alone.
Once you have disabled missiles, beam and the ion weapon, the flagship is pretty much toothless. Now you can start to kill of the remaining crew. Beam into the cockpit and kill the pilot. The other rebels won't be able to help him, cuz the doors are locked due to hacking. Repeat until everyone (except the laser guy) is dead. Then finish the flagship.
The systems will be repaired when the next phase starts, but the ship will no longer be able to repair itself during combat. Also the weapon speed and dodge chance are reduced, because the crew is gone. You should have no trouble now.
Minor correction:
The weapon speed doesn't change at all, because they are artillery systems and cannot be manned by crew.
They made the Flagship artillery crew look like they are manning the system, but they're actually not.
Boarding on normal and easy means missiles aren't an issue and makes the boarding on the phase 3 a non issue because they should have no or few crew.
Hack their shields. This makes it easier to get crew kills and of course makes it easier to damage shields and missiles. Even if you have crap weapons, hacking can carry you through. Look up hacking defense drone dodge for phase 2.
Cloak missiles in phase 1 and 2. On phase 3, don't cloak the first missile volley. Instead cloak the second so you also dodge the power surge.
To facilitate getting these things, you need to get be getting as many jumps as you can and find as many stores as you can (assuming you have scrap or stuff to sell). Plot your journey through sectors to reveal as many beacons as possible. Knowing where a store is is very valuable.
Ideally, you want to get to the exit beacon just before the fleet does. If you have cloaking or can kill fast (engines charge faster if the enemy dies), it might be a good idea to get extra jumps in exchange for "diving". Also if the exit beacon is in a nebula, there won't be an asb and it'll be an ion storm instead which is much more manageable.
Get boarding with mantis and rock
Have weapons capable of dealing with at least 6 shield (only need 4, but shots can and will miss)
Get cloaking lvl 1
Board missiles, kill the dude, break the system, repeat with all weapons systems.
If you have 4 tile boarding, take out medbay and leave all but one dude.
Take out shields
Attack.
https://steamcommunity.com/sharedfiles/filedetails/?id=3445463160
In that one, I was able to start a fire in Medbay with a Fire Bomb, right after the Flagship came out of one of it's cloaks. When repairers were sent to put it out, I used Mind Control on one of the repairs to interfere with the firefighting. While they were fighting in Medbay, I sent a second Fire Bomb into Medbay. With Medbay destroyed and on fire, no one was getting any more healing, so I finished them off with a few more Fire Bombs and Mind Control fights.
Level 2 Mind Control on its own is enough to clear out most of the interior Flagship crew. Level 2 lasts just long enough for two other crew to gang up on him and kill him just before the Mind Control wears off.
Weapons that do system and/or crew damage without doing hull damage are great in phase 1- Small Bomb, Fire Bomb, Breach Bombs I and II, Fire Beam, Anti-Bio Beam. They help you kill the crew in the turrets without doing much hull damage, so you don't destroy the Flagship before you get a chance to kill the interior guys. Of course the same weapons are great on the interior guys, too.
Hacking locks doors to the hacked room, so that's useful for holding crew in place so they can't run to Medbay before you finish killing them. Fires also spread faster in hacked rooms, and breaches (and systems) take twice as long to repair. If you hack Shields, that's a good place to start your Mind Control fights- be sure to power down Hacking to let crew in, then power it up to lock them in. If you damage Shields, then Mind Control crew there, they will send extra guys, filling it up really nicely for you to bomb them all.
Hacking the Shields room also isolates Piloting. Sometimes that makes Piloting a good place to create chaos, because crew will have to get through two sets of hack-locked doors to get back and forth from Piloting.
I'd look first for Hacking then Mind Control. It depends in part on availability and usually I'd take first available. Even if I have a choice, there are occasions where I'd take Mind Control first if I had few drone parts. (I'd also take a mediocre but usable weapon over both systems, if I have choices.)
Hacking is a versatile system that helps any ship, and it's almost always the first system I'd prefer to have. If your firepower is weak, then using Hacking on Shields/Piloting/Engines helps a lot.
Whether Shields or Piloting/Engines is the better target is circumstantial. Reducing enemy evasion to zero removes the randomness, lets me know what will hit where, and that's especially useful if I have bombs or missiles. It's also something you can do with just level 1 Hacking.
Hacking Shields is great when you are using beam weapons, and generally allows for greater damage upside, but you remain at the mercy of the luck of evasion (unless you have done something else to screw with evasion). It really needs to be level 2 Hacking for 2-3 layers of Shields, and level 3 for 4 layers of Shields. (At 5 layers of Shields, level 3 Hacking will only bring them to zero for the tiniest fraction of a second; functionally it will drop them to 1.)
Even if your weapons are weak, it is still a consideration to use Hacking against enemy Weapons. 1 or 2 points of damage to enemy Weapons when they are hacked can potentially be crippling. If your weapons move from modest to good, you can go to Weapons hacks all the time.
Mind Control is usable on enemy pilots to reduce ships to zero or near-zero evasion, which is a great help to weak weapons, particularly those that have few shots per volley. The timing has to be precise- using it the instant your first shot is about to cross the Shield threshold- because when other enemy crew make it to the cockpit to fight, the cockpit is no longer considered empty and evasion shoots back up. Of course Mind Control doesn't help against automated ships.
Mind Control against enemy pilots also provides less (but still some) help when ships have upgraded Piloting. On the other hand, if that first volley can do any damage, the crew assigned to fight the pilot can get re-directed to repairs, and the mind-controlled pilot is free to destroy Piloting by the time your next volley is ready.
The great thing about both Hacking and Mind Control is that they are so versatile, and as your weapons change, the way you use the systems can change.
Drone Control can add offense to weak weapons. But offensive drones require so much micro-management to use effectively. Picking up Drone Control to help weak weapons would be a desperation move for me.
Circumstantially, if you're trying to run a gunship but are having trouble finding the guns, it's always a consideration to stop trying to be a gunship and become a boarding ship instead. I prefer gunships to boarding ships so that would be another one of those desperation moves for me, but it's still always something to remember.
Here's an example where I tried to outgun the Flaghip. Would you say worked out badly for me?
https://www.youtube.com/watch?v=_4jTYvVkFqU&list=PLYGAjVZPcf_Ts6tR1LFk3LxEG040ly9EI&index=25