What am I doing wrong? (Noob)

[Neutronium]

Ok,

I have only the Kestrel and Engi ship.

I arrived yet again at the flagship with the following

Max (4) shields
All but 2 engines
upgraded helm, doors, sensors etc.

Full hull

Scrap arm, auto-reloader

Burst 2
Burst 1
Heavy 2
Pike Beam

Never saw a teleporter or pre-igniter all game

systematically targetted all weapons, did phase one, 75% hull

Got flattened by drones, all weapons targetting drone system couldn't slow them down....

What am I doing wrong?

[stylesrj]

Did you target the missile launcher and the crew operating it constantly? Because that's always the biggest threat on the Flagship.

What other systems did you have on your ship? You said you didn't have a teleporter but did you have anything else besides that like Cloaking, Mind Control, or Hacking?

Most strategies rely on removing all the crew from the Flagship in Phase 1 where there are no bothersome power surges. There are ways of doing that without the teleporter. Fire is one such method, mind control is another. Hacking too if you hit their shields constantly with everything and you hack their medbay.

They take damage, they fix the system and then run off to the Medbay, which you power down the Hacking Module for. Once they're in, you power it up and activate it and watch gleefully like a sadistic person as the nanobots tear them apart (unless the crew breaks out)

Keep the guy in the triple laser station alive (it's the gun to the left of the shield room. Not the far left. That goes away after Phase 1). You don't want any nasty surprises from the Flagship losing its crew.

[5thHorseman]

I assume you're playing on Easy or Normal? On those, step 1 is frequently killing the missile guy and disabling the missiles, unless you can just kill the ship quickly.

With 5 regular and 2 heavy shots, just going for the kill is probably preferable. I'd wait for all to charge, fire the 5 lasers at the shields, and follow them with the 2 heavys immediately (before they hit but after they've all fired). Then as soon as the shields are down, pike beam from the engine room up through to the cloak, hitting 6 rooms. With any luck you'll do 6-10 damage and take their shields down to 2 or 3. Repeat that 3 times and you've killed them. Repeat THAT 3 times and you've won the game.

But yeah, knowing what else you have is important. Hacking can do wonders on the shield, or on their hacking, but hacking doesn't work great in the 2nd phase and you can't immediately use it in the 3rd. Mind control works great but if you kill the crew, it's less useful Drones and cloak will make your day much easier too.

[Neutronium]

I think the missile launcher is the inside right one, correct? If so I always go after that one first.

Good tip to leave one of them alive.

I've been playing basic (not advanced) while I learn it. Is that a mistake?

Sounds like no matter what you need something beside weapons to take it down. I think I'm also not salvoing correctly.

The 2s are level of the weapons - there's only 4 equipped on my ship.

Thanks!

[stylesrj]

I think the missile launcher is the inside right one, correct? If so I always go after that one first.

That's always the biggest threat. Unlimited potential to do 3 damage, cause a hull breach and start a fire in your Life Support? Hell no! Missiles have to go!

Good tip to leave one of them alive.

But then again, if you have Breach Bombs, you can kill all of the crew. Just make sure to put bombs in the Missile Launcher, Shields and Pilot.

I've been playing basic (not advanced) while I learn it. Is that a mistake?

Well Basic doesn't have all the cool toys like Clone Bays, Mind Control, Hacking and Lanius crew.

The Flagship also plays out differently. Phase 1, they'll try and randomly hack a system on your ship and Phase 3, they'll try and mind control someone. If you have Mind Control of your own, use it to counter Mind Control. (Just make sure to power down Mind Control in Phase 1 before the Rebels hack your ship. Once they've hacked something though, power it back up if it's not being hacked)

Sounds like no matter what you need something beside weapons to take it down. I think I'm also not salvoing correctly.

Salvoing is easy. Start with ion weapons or missiles or bombs to take away shield layers, use Burst Lasers to deplete shields, then anything else is used to do heavy damage to the shield. Like beams. Beams always go last or when there's no shields to get in the way.

[Tharsis]

You should always try to get cloaking as well. +60 evade is very helpful. As stated previously, kill all crew except the triple laser guy and it will be much easier. Any damage to a system and it will stay damaged. Just one damage to the drone control will stop that boarding drone. Fire all lasers at the shields at once (fire the heavy a bit after the others so it goes through the shields) then pike the most rooms you can.

From your post, you didn't do anything wrong. The RNG was just not very helpful.

[Twinge]

Were you using auto-fire? Turn it off - pause and fire your weaponry together in a volley. standard lasers first, then heavy lasers, then beams when their shields are down. Also consider taking out their defenses and ignoring their offenses - if you have a reasonably strong weapon setup (like the one you described), you'll often end up taking less damage by just killing them quickly (taking out Shields/Cloaking/Evasion) versus trying to take out their weapons.

[Feculator]

In FTL it's also important to know what you DON'T need. A 4th shield layer is a luxury. Upgrading the engines gives diminishing returns (+3 evade instead of 5). You should also consider selling the scrap arm for 25 at sector 7, especially if that let's you get something cooler. A level one O2 room is usually enough, what's more, you can reroute its power to your engines when there's shots incoming and then back again (in general you shouldn't be afraid of switching O2 off if you need power somewhere else for a while). Only keep your medbay on if you actually need to heal guys.
Teleporter is indeed good against the flagship. Missile launcher is top priority, then the left-hand ion gun, then the beam gun on the right. When taking out the flagship's weapons in the first phase you'll only need your boarders and a missile or a bomb to speed things up; you DON'T need power in lasers/ions/shield-busting gear, unless it's something powerful and reliable even if the flagship evades a few shots. You can switch off defense drones once the missile launcher is down. Leave the laser guy alive (with no crew, an advanced AI takes over which is probably worse). With three shields you should be safe, letting you take your time for the next stage; here you can power down your other defensive measures, shields will soak up everything.
Now your job is to kill the rest of the crew: fight the pilot, then when injured guys run to the medbay, attack it with your weapons. Once the the medbay is wrecked, you'll have an easier job. I wouldn't advise fighting in the medbay (even once it's wrecked), because it is 2x2, the flagship has blast-doors, so your boarders will most likely get overwhelmed and trapped. Rockmen+fire is good though. Without those, however, you should rely mostly on good management of your boarders and teleport cycles (beware: you can't retrieve crew from cloaked ships!), and killing near-dead enemies with your guns. Make sure you don't accidentally set fire to/destroy their O2 and make the laser guy suffocate. Have 4 guys on the flagship at this stage if you can, and the door-room is almost as high-priority target as medbay.
With the crew dead the rest of the fight is much easier, you can run them around the ship to tear it up, you can start fires etc. Just take down the zoltan shield in phase 3 ASAP

[Feculator]

BTW, you maybe right in learning the nuances one step at a time, but advanced content doesn't make the game harder. Hacking in particular is a great addition, you can defend against it with a drone, and even if you don't have one the enemy doesn't always use it on anything critical (for example if you are boarding the flagship you can live with a hacked weapon room). Hacking the flagship's medbay on the other hand is one of the best ways to take out the crew (you don't even really need a teleporter if you couple it with fire weapons and/or mindcontrol).
Fire the hack drone, once it latches on, unpower it (it doesn't lock doors this way). Then, when enemy crew comes rushing in because their medbay is on fire/damaged/full of boarders/attacked by a mindcontrolled thrall, power up the hack and punch it! Fried rebel ready to go.

[Jhffmn]

I always pick up stealth or drone control with a defensive drone 1. Also not a fan of pike beam at all.

I don't consider myself to be very good at the game but I've beat it with most of the ships on normal difficulty now and unlock everything but slug c so far. If you are doing things right the flagship should be easy. You've seen enough shops that it takes a pretty terrible run to leave you without the resources to end the game.

I lost a run to the flagship not too long ago go so it can still happen but I got like no scrap or weapons all run, but it takes a lot of really bad kuck that point even if you are playing poorly.

To salvo, wait till your weapons are all charged. Pause the game, fire your ion first. The second they hit pause again fire all lasers, and the second shields are down, pause and target beam weapons.

It sounds like bad RNG wasn't your issue though.