There's basically only two ship setups you can have that can beat this thing. Either you have maxed engines or cloak (preferably both) with two Mantis crew members, or you are straight up not going to get past the second form. And in the off chance you do, the last form launches 6 missiles at a time, so shields are COMPLETELY fucking worthless.

Is it really that odd that you need to have your defenses beefed up for a protracted battle against the enemy flagship? As long as you DO have your engines at or near max with skilled crew on them and a few shield bars, it takes the boss ages to do any serious damage to you. So as long as you have some way to get past its shields, you should be fine. I beat it on normal last night with only 4 crew, a small bomb launcher and 3 basic lasers. The entire enemy crew just ran into the shield room when I started bombing it and died in a series of explosions and fire.

@EToaster said:

Is it really that odd that you need to have your defenses beefed up for a protracted battle against the enemy flagship? As long as you DO have your engines at or near max with skilled crew on them and a few shield bars, it takes the boss ages to do any serious damage to you. So as long as you have some way to get past its shields, you should be fine. I beat it on normal last night with only 4 crew, a small bomb launcher and 3 basic lasers. The entire enemy crew just ran into the shield room when I started bombing it and died in a series of explosions and fire.

The problem is that you need to be specced in the EXACT right way with the EXACT right makeup of crew and the EXACT set of weapons necessary to bypass its shields or you have absolutely zero chance of winning.

The first phase is easy. The second phase is retardedly difficult because it has infinite 150 health 2 star combat Mantis strength drones that it will repeatedly send onto your ship until you die. The boarding drone has no cooldown, so the instant you kill one it'll just send another. Can't make it miss either, because the flagship has 100% accuracy. Also, it causes a breach in whatever room it hits, so now you're running out of fucking air. None of this would be so bad if it wasn't spamming 10 drones at a time whenever the fuck it wants. Can you prevent this? FUCK no. If you destroy the system that controls that, it's instantly repaired by 4 crewmen who have health that regenerates faster than 2 starred Mantis crewmen can do damage to it. The only weakness the fucking thing has is that you can destroy those weapons and they can't regenera-OH WAIT THEY CAN AND DO ON PHASE CHANGES. So while all this shit is going down you're desperately trying to shoot missiles - the only things that can hurt the fucking Flagship because of 4 bars of shields - except OH WAIT it also has maxed out engines and perfect crewmen to man the stations. Immortal crewmen, I might add.

But hey, you fight past that and somehow manage to beat it. Now you're out of missiles and now it shoots lasers that can pierce 4 bars of shields, runs along the length of your ship, completely disable systems in a single hit, cause breaches and fires that quickly spread IN SPITE OF THE FACT THAT THERE'S NO OXYGEN. You can't pierce FIVE bars of shields because you're out of missiles, but guess what? It just shot 6 of them with pinpoint accuracy at you. You just took 20% of your health in completely unavoidable damage that's not based on any system, and it will fire said missiles every 10 seconds until you die. You literally have, at MAXIMUM, a minute before you're dead. Except you can't regenerate from the first 2 phases because every repair station is conquered instantly and if you try to save them the flagship gets in range (which, by the way, is considered 2 adjacent systems away) and the game's over. You just wasted 2 hours wading through a piss-easy game until the last boss shits on every rule of the game you've learned and rolls over you like that fat kid who the teacher said had to play Superhero with you, except his superhero is stronger than pre-crisis Superman.

@Terramagi: lol, Damn calm down Terramagi.. gets some decaff it'll be ok.

Speaking of the rebel boss tho.. I've beaten it twice on normal.. each time with a different build. I've never found it really that hard.. challlenging yea.. but i think the hardest part of this game is Sector 3 and 4.. the part where you don't really get a ton of scrap yet.. but the enemies start showing up with lvl 3 shields that'sII the hardest part of the game for me.. past that it's not to bad.. still tough.. But defiantly do able.

1st Build was - 2 Burst Laser II 1 Burst Laser I and Starting Missile Launcher on the Original ship.. I demolished the rebel boss ship.

2nd Build was - 2 Burst Laser II Meta bomb and then that Huge Halberd laser that comes with the federation cap ship... that one wasn't as easy but still not to bad.. i just had to be a little more strategic with my weapons.. but all good..

trying a completely different build with the ingi ship next!.. tho there much tougher to play through.. not as bad as the Zoltan.. but still tougher than the first two ships.

Zoltan Ship.

2nd Layout

Maxed Shields.

Ion Cannon 1

Ion Cannon 2

The starter Beam which name I can't remember

a normal bomb

Defense drone.

Problem solved. In fact, the ion cannons took out their shields so quickly that I could take out their weapons, I think I only got damaged on my hull once through all 3 rounds.

@Terramagi: I agree that the flagship maybe breaks one or two rules too many. Triple-firing ions AND triple-firing missiles is a little excessive, and unfortunately makes a mockery of your defense drones, which is unfair when up until that point defense drones are adequate defense against any missile launcher (and of course bombs are the fair counter for a defense drone).

You don't even need 2 maxed out Mantis crew members. The weapon rooms are so poorly defended that any 2 crew members (other than Engi or Zoltan) are fine. The boarding drone is definitely annoying, but if you have a defense drone, they seem to have a pretty good success rate at shooting down boarding drones before they enter your ship. Admittedly, if you don't want to teleport into their ship, your options aren't as convenient; you can either take time lowering their shields and attacking weapon systems individually, or you can forgo attacking the weapons and just pummel the shield room nonstop, in a race to kill the flagship faster than it can kill you. Granted, if you go for the second option, you need a spectacular weapon combo and you probably need the cloaking device to not die to all the missiles/drone attacks.

So yes, going into the final fight, you do need either the cloaking system or the teleporter, but that late in the game, you really should've acquired one of them at least. Your complaints about running out of missiles or whatever against the enemy's strong shields don't seem like the huge concern you make them out to be; relying on missiles to take out shields becomes less reliable in the late game as more ships have defense drones, so you need to prepare your ship for that, especially when you learn that the 2nd phase of the Flagship always has a defense drone. When you're getting near the final sector, it helps to rely on ion weapons and burst lasers, with maybe one slot reserved for a bomb or a beam weapon.

I do agree that the Sector 8 map still really needs some work because it is too stacked against you, but I doubt they'll change it much at this point. Most of the beacons are fights against powerful Rebel ships to begin with, and obviously the Flagship is pretty effing hard, so why complicate things by having the Rebels slowly "take" beacons? What's the point, when most beacons are already fights anyways? You're right, in that it ends up screwing you out of repair stations, which is ridiculously unfair since you WILL need to repair between Flagship phases. And there aren't even that many repair stations to begin with, and they're often inconveniently placed so you can't even take advantage of more than one of them anyways. I feel extremely lucky when I get to use even ONE repair station in the final sector.

Finally beat it.

Everything I said still applies. The only reason I won was because I managed to get a Breach Bomb and about 30 missiles going into Phase 2, and slowly but surely killed their entire crew, save one, with them. Plus I was lucky enough to have a store NOT die, and be located directly next to me so I could repair my 20% hull back to full and buy about 5 more missiles. That was enough to drop their shields and bridge with Breach Bombs and, since they had no crew left to repair, basically crippled it to the point where I could 15s cloak through the unavoidable missile spam and whittle them down with the starting 3 shot laser.

I have enough fun dying before getting to the boss that I don't really care that the boss is a cheap piece of shit.

I think it's a bit of a bummer, but I have put my focus on finding new ships for now. The boss is very beatable when you go for a very specific build, but I feel that kind of goes against what the game is. You should have more valid options for beating it.

@thabigred said:

I have enough fun dying before getting to the boss that I don't really care that the boss is a cheap piece of shit.

If I die on the way TO Sector 8, I don't have a problem.

Dying to the boss, conversely, is fucking bullshit because it wasn't a series of unfortunate events, it was some designer going "y'know what'd be neat? 8 fucking missiles every 10 seconds."

Like, losing because two of my crew members were on a boarding mission, had killed the entire crew, and then had the FTL drive kick in while having half the doors of my own ship open to the vacuum of space due to a solar flare knocking out door control, and then my remaining crew slowly roast alive is fun, because I can imagine the two Mantis on that ship were like "FUCK THAT NOISE" and stole the mostly intact Rock ship to become bandits.

Losing because the Flagship has infinite boarding droids that are guaranteed to cause hull breaches is, conversely, not.

it's a hard ass fight, no doubt. I started playing as a Mantis ship (type 2, so pure boarding), but half way through, all my mantis' died and I had only the repair guys. I had to improvevise and switched to two blasters and a hull attacker. I managed to do decently by attacking his weapons with the two blasters, hoping all 4 attacks hit so I could beam the weapons instantly. Eventually I killed the repairmen (they're sectioned off). I got to the final form doing this, and was doing decently until I ran out of drones and couldn't repair anymore. I also used stealth, had maxed shields, decent engines (wish I maxed them instead for the dodge chance). The thing that kept me alive was using a defender 2 for the missiles. I should have won, damnit. Also, good use of stealth. I also had 2 Voltrons to manage all of this. I also didn't have a full crew which made it more difficult, I only had 6 guys.

Got him to about 20% and had the entire crew killed. :(

@Terramagi said:

@thabigred said:

I have enough fun dying before getting to the boss that I don't really care that the boss is a cheap piece of shit.

If I die on the way TO Sector 8, I don't have a problem.

Dying to the boss, conversely, is fucking bullshit because it wasn't a series of unfortunate events, it was some designer going "y'know what'd be neat? 8 fucking missiles every 10 seconds."

I've heard a litany of ways people have completed the final boss, so when you complain about the boss being a cheap piece of shit I have to think maybe you should change your play style to fit beating the boss instead of complaining about the boss being cheap.

@thabigred said:

@Terramagi said:

@thabigred said:

I have enough fun dying before getting to the boss that I don't really care that the boss is a cheap piece of shit.

If I die on the way TO Sector 8, I don't have a problem.

Dying to the boss, conversely, is fucking bullshit because it wasn't a series of unfortunate events, it was some designer going "y'know what'd be neat? 8 fucking missiles every 10 seconds."

I've heard a litany of ways people have completed the final boss, so when you complain about the boss being a cheap piece of shit I have to think maybe you should change your play style to fit beating the boss instead of complaining about the boss being cheap.

"The problem with the final boss is that you have to configure your ship in just the right way to have a shot at killing the boss."

"So why don't you just configure your ship in just the right way?"

Reading comprehension really is not your forte, is it.

@Terramagi: That still doesn't change the fact that half the things you complain about as being "cheap" and "bending the rules" are simply not true.

You complain about the "OP boarding drone" when it's exactly the same model all other ships use, all of them leave a breach and all of them stop acting as soon as you take out drone control (even on the flagship). Taking out drone control in second phase will also slow down the recharge on the energysurge drone rush. But the flagship boarding drones are not different then any other boarding drone in the game.

In third phase it's the teleporter that's shooting out tons of lasers, that's something you can mostly absorb or just evade with cloak. But other then that there are tons of approaches for killing the flagship, they all depend on what kind of tools you have at hand. Double defense drone+ some decent dodge will make that triple missile launcher a joke, add an additional hull repair drone and the whole fight becomes a joke.

But if you can't even take out the triple missile launcher then you have been ill equipped, a simple level 1 teleporter is enough to kill it. Even if you don't have enough laser weapons to punch trough the shields, then you should have enough missile weapons/bomb teleporters to grind them down. Yes sometimes you reach the flagship and know that you lack the tools and resources to beat it, but that's in the nature of the game due to the massive dependency on RNG.

To be fair I almost beat the boss with a really atrocious setup; Red-Tail (which is easily the best ship in the game, though I seem to have terrible weapons drop luck with it) with 2 basic lasers, Hull laser mark 2, Halberd beam, Defense Drone 1 and Anti Personnel Drone; 3 shields, no cloak, if he hadn't hit my weapons with his second doom burst I'd have won.

I was JUST about to kick the 3 stage flagship's ass and i jumped too far for repair and it reached the base before i could catch up with it...fuck me

And now I unlocked the Stealth bomber got all the way to Sector 6 lost my 4 mantis death squad to a bone head move on my part.

Got to Sector 8 with a sweet build, destroyed stage 1 of the boss no problem. Then failed on stage 2, but had I had that boarding party i wouldn't have gotten my ass handed to me...

goddamnit this game is the only game in my recent memory that has made me act like a 10 year old having a fit and throw shit across the room lol

I just had a really tense moment with the 3rd phase of the final boss. It was my first try with the stealth cruiser, and things were going really well, but I lost my 2 mantis before I reached the boss...I think the AI is learning my tricks, because they bombed my medbay while they were returning from a raid to heal up. I also lost the 2 spare crew members I was boarding with in the first phase because the boss was destroyed by a fire when I didn't expect it.

Anyway, I had a halberd beam, dual laser, and small bomb launcher. I went into the third phase and ended up retreating because I had most of the remaining enemy crew on my ship, and a lot of my systems were damaged. Then I realized I only had 1 missile left, and if I didn't manage to land it on the shield generator, there would be no way for me to pierce the shields at all. Firing that thing off and seeing it land was such a relief. Of course, while the credits were rolling, I realized that I could have sent in my support crew to smash the shield generator, but thankfully that wasn't necessary.

@Twoheadedogr: How on earth did you beat the boss with just two burst lazers and the starting missile launcher?

@9cupsoftea: Have a Good defense, and go for the shields first is my tactic.. and make sure you fire all weapons at the same time to or its next to impossible to get them shields off line..

I've beaten the boss four times now (had the game since a couple of days after release and have played about 12 hours) using vastly different weapon setups

- Zoltan 1 - Halberd, breach bomb, 2 x burst laser 2, cloak

- Slug 1 - Burst Laser 3, basic missile launcher (don't remember which), 2 x anti bio beam, teleporter w/ 2 veteran Mantis, cloak

- Federation Cruiser 1 - breach bomb, ions x 2, burst laser 1, teleporter w/ 1 veteran Rock, one nub Mantis (lost my 2 x veteran Mantis party), boarding drone

- Slug 2 - ion bomb, burst laser 1, heavy laser 1, healing burst, teleporter w/ veteran slug and veteran mantis, cloak, 2 x defence drone 1

Last one was the easiest, I think I got hit twice across all three stages. The Others were slogs, particularly the federation cruiser, but all were manageable.

I've had plenty of failed attempts too of course, and sometimes the loot doesn't go your way, but there are many different ways you can spec and still be viable by just being ready to adapt to the loot you get; my Slug 2 game, for example, I never found a single weapon dealer but kept finding drones, so I improvised and played defensively while using my teleporting death squad and healing bursts to slaughter enemy crews instead of my usual preference of smashing shields down with ions and multiple burst weapons.

i fined most of that game is luck drops. i only say this because i have gone threw the game and never received a weapon drop or did not have money to buy one. That being said its hard to beat the boss with 4 one shot lasers :-)

@AbeBroHamLincon said:

i fined most of that game is luck drops. i only say this because i have gone threw the game and never received a weapon drop or did not have money to buy one. That being said its hard to beat the boss with 4 one shot lasers :-)

You will always get enough scrap to buy a weapon, just save money. Now if none of the shops actually have weapons, that's when you're just straight up getting fucked. Anecdotally with the Red-Tail I seem to have the worst weapons drop luck, though it seems to be the best ship otherwise.

Burst lasers are greeaaaat. I beat the game with the Kestral with cloak, two burst laser 2s, an ion beam and an ion bomb. I didn't drop past 95 percent hull strength against the final boss, just an absolutely killer load out.

I beat it a second time with the Federation Cruiser with one burst laser 2, an ion beam, a pike beam and the cruiser's beam - no cloak, low upgraded engines, but level three shield and defense drone. It was close, but totally doable.

I love this game.

Still haven't finished it after 20 hours...

I just beat the boss for the first time (on easy) with probably the worst build I've ever reached him with. Shields level 3, engines leveled just under halfway, starting missile, starting burst lazer, ion blast II, anti ship drone 2 and only 4 crew members (one of which died on second form).

I have to agree the boss is poorly designed. I've had far far better builds than this and the only reason I managed to win this lazily was because I knew what weapon the boss does most damage with and how the boss strikes in each form. I really hope they change the boss - it's too easy to die with a good build, and too easy to win if you know a few tricks.

On runs where I did pretty poorly and didn't design my ship with the end boss in mind I still managed to stalemate it. It could not kill me, but I couldn't kill it either.

You make a big deal out of the missiles, but the ships throughout the game shoot more and more missiles as you progress, and missiles do actual damage that cost money to repair (as opposed to absorbing lasers with shields), so you're pretty much playing like a retard if you haven't already made yourself survivable against lots of missiles.

@Terramagi: I had neither maxed engines, cloak nor 2 mantis crew members and I beat it easily. So, you you're wrong. There are numerous strategies to beat that thing.

I was surprised how easy the first form was. Then *INFINITE DRONES* and I lost too many crew members to stand a chance, so I said eff it.

I'll never beat this game, and I'm now okay with that.

I did it with the Engi ship, two drones, the ion cannon and a telebomb and teleporter. My shields were 3 and my engines were about the same.

So i ported over my 1 mantis crewman and my 1 rockman. to mess things up aiming for the misses first with a bomb throw in before they ported.

And just worked hard to get through. i got lucky in the end one shot of anything would have destroyed the ship or killed my last engi.

@Cretaceous_Bob: But the boss's missiles really are a cut above anything else. They fire 3 at the same time, with good accuracy, and a high chance of fire and breach. If you don't evade/cloak and get hit by all of them, your ship is pretty much cooked.

@9cupsoftea said:

@Cretaceous_Bob: But the boss's missiles really are a cut above anything else. They fire 3 at the same time, with good accuracy, and a high chance of fire and breach. If you don't evade/cloak and get hit by all of them, your ship is pretty much cooked.

The only thing that kept me alive as long as I was able was an evade score near 50% when everything was optimal and my ship wasn't already a smoldering wreckage barely holding on.

Maybe so, but on the other hand, the Imperial flagship has that really exposed bridge that an A-Wing could easily crash into, causing the entire ship to fall out of the sky.

@9cupsoftea said:

@Cretaceous_Bob: But the boss's missiles really are a cut above anything else. They fire 3 at the same time, with good accuracy, and a high chance of fire and breach. If you don't evade/cloak and get hit by all of them, your ship is pretty much cooked.

I had missiles that started fires and those weapon rooms are separate from the rest of the ship, so they can't be repaired by anybody except the single dudes already in the room who are also conveniently cooked by the fire.

Breach bots can totally neutralize the missiles too.

The real motherfucker about that ship to me is the 4 shields coupled with defense bots.

@Cretaceous_Bob: Yeah, but that's the thing. Unless you know how powerful the weapons are, and which specifically is dangerous, then the fight is far too imbalanced. I have to agree with the OP. There's a nice push-pull and resource management (reminds me of theme hospital) to the combat when you're fighting tough ships, but with the rebel flagship it's all about neutralising that one-hit-kill weapon.

@Cretaceous_Bob: But the boss's missiles really are a cut above anything else. They fire 3 at the same time, with good accuracy, and a high chance of fire and breach. If you don't evade/cloak and get hit by all of them, your ship is pretty much cooked.

@BisonHero said:

@9cupsoftea

@Cretaceous_Bob: But the boss's missiles really are a cut above anything else. They fire 3 at the same time, with good accuracy, and a high chance of fire and breach. If you don't evade/cloak and get hit by all of them, your ship is pretty much cooked.

I'm pretty sure the final boss' missiles are just standard missiles with low fire chance and low breach chance (just like the Artemis missile that the Kestrel starts with). The only reason it seems to start a ton of fires and breaches is because launching 3 at once tends to increase those odds.

I'm not too sure about that. Whenever I've had the hull breach missile or a more powerful missile launcher, the missiles themselves look longer and bigger than the basic artemis-fired missiles. The rebel flagship missiles (if I'm remembering right) are also bigger, I think.

The Flagship missiles look like standard artemis/leto/pegasus types, but they do seem to start fires at about a 50% clip (as opposed to 20% or so for the others), certainly much more dangerous than any other weapon on the ship.

@BisonHero said:

@9cupsoftea

@Cretaceous_Bob: But the boss's missiles really are a cut above anything else. They fire 3 at the same time, with good accuracy, and a high chance of fire and breach. If you don't evade/cloak and get hit by all of them, your ship is pretty much cooked.

I'm pretty sure the final boss' missiles are just standard missiles with low fire chance and low breach chance (just like the Artemis missile that the Kestrel starts with). The only reason it seems to start a ton of fires and breaches is because launching 3 at once tends to increase those odds.

I'm not too sure about that. Whenever I've had the hull breach missile or a more powerful missile launcher, the missiles themselves look longer and bigger than the basic artemis-fired missiles. The rebel flagship missiles (if I'm remembering right) are also bigger, I think.

Just wanted to say I beat the rebel flagship on my first try. Granted it was my third playthrough, but I only missed fighting it because I didn't understand the Flagship will be in range in X turns thing the first two times. The first time I thought it meant I would automatically be attacked and simply had X turns to prepare. The second time II thought I had to be on the Base tile when turns ran out.

I won using an Engi ship wwith no cloak but a generous amount of fire bombs.

@9cupsoftea said:

@Cretaceous_Bob: Yeah, but that's the thing. Unless you know how powerful the weapons are, and which specifically is dangerous, then the fight is far too imbalanced. I have to agree with the OP. There's a nice push-pull and resource management (reminds me of theme hospital) to the combat when you're fighting tough ships, but with the rebel flagship it's all about neutralising that one-hit-kill weapon.

No it isn't. I've been killed by lasers, missiles, breachbots, beams, and fires by that flagship. It tests your ship's ability to handle all of the gameplay concepts that were present throughout the game thus far.

I've beat it twice having neither full engine power or cloak. Just a lot of crew and firepower. My spare crew patched up the holes/put out the fires and my weapons took the flagship apart. It's not a fight you'll win on the first time round unless you get a lucky run...it's best to know it's phases and when and where to hit it.

The first form i usually hit the missle weapon/ion once it's shields are out. On the second you get the drone system and the third seems to be the easiest...never had an issue on the third form.

@Cretaceous_Bob: Fair enough. It's just my experience though, like I said before. I had awesome builds get hammered by the flagship because I played the game focusing on everything, whereas I defeated it fairly easily with a poor build just by going after that weapon (and drones on the second form, slightly).

@BisonHero: Yeah, you're right about the missiles. My mistake.

@J12088 said:

I've beat it twice having neither full engine power or cloak. Just a lot of crew and firepower. My spare crew patched up the holes/put out the fires and my weapons took the flagship apart. It's not a fight you'll win on the first time round unless you get a lucky run...it's best to know it's phases and when and where to hit it.

The first form i usually hit the missle weapon/ion once it's shields are out. On the second you get the drone system and the third seems to be the easiest...never had an issue on the third form.

Knocking out the drone system actually doesn't do anything to the doom waves, with upgraded doors breach drones are rarely an issue; so the order remains Shields > Missile Launcher > Engines/Pilot even on that phase. The last phase can be quite difficult if you have bad luck with dodging assuming you don't cloak; but you could dodge everything or all the hits could land on systemless rooms and you'll likely be fine.

Taking out drones gets rid of its boarding drone and its 2 basic drones that are always attacking, you, which lowers the effectiveness of its drone swarm. Honestly never had too much issue with it, though. Most of the drones are beam drones that can't do any damage as long as I've got 1 shield. Evasion really is king in this game, and I've always prioritized having 52/55% evade by the time I reach the boss.

.On a serious note fucking kill the entire crew on the first form, it is super easy if you take the time to do it since you can take out all the weapons.

The rebel ship can SUCK IT because I DESTROYED IT. It's pretty tough, but manageable. I didn't lose one man! I went in thinking that my weapons were underpowered, but was able to take down his weapons with my boarders, and whittle at his hull. It turns out that the ion gun is the most useful thing ever, so I suggest you find one of those.

@LordXavierBritish said:

.On a serious note fucking kill the entire crew on the first form, it is super easy if you take the time to do it since you can take out all the weapons.

Killing the entire crew made it harder! The weapons regenerate instead of requiring repairs, if possible try to leave 1 or 2 members alive on the flagship. That way you can keep multiple systems broken without having to seriously spread out your attacks to keep everything in check.

@MysteriousFawx said:

@LordXavierBritish said:

.On a serious note fucking kill the entire crew on the first form, it is super easy if you take the time to do it since you can take out all the weapons.

Killing the entire crew made it harder! The weapons regenerate instead of requiring repairs, if possible try to leave 1 or 2 members alive on the flagship. That way you can keep multiple systems broken without having to seriously spread out your attacks to keep everything in check.

The easiest one is one of the middle gunners. Probably the one on the left. Since it's isolated, and the crew doesn't respawn (though they do regenerate health) through phase shifts, the only thing he can actually repair is his laser gun. The one on the middle right is obviously the missile launcher, which you want out because... y'know, missiles. And the two on the side are automatically destroyed during phase shifts.

Killing all of them has the ship's AI kick in, which is basically like the auto-scouts you fought through the game except it repairs as fast as an Engi, shipwide.