Cloaking is so useful against the boss. In the first stage you can use it to avoid his missile barrage at the start of the fight or to give your shields a chance to recharge later on. During the second and third stages, just look out for the words 'Power Surge Detected' to flash up on your screen and get ready to avoid a lot of damage. Even just level one cloak is enough. In fact, for the later stages it's actually better as it ends faster and starts recharging faster.

@pantyfire: I just beat the boss for the second time today.

I wrote:

@pantyfire: I just beat the boss for the second time today.

...and that makes three. That must be my most successful day of ftling yet. Three victories and two new ships unlocked. Set phaser to smug.

I DID IT. I FUCKING DID IT. FUCK YOU GAME. 

I literally stood up and punched the air. 

Kinda underpowered in the end. 
2x Burst lasers mkII
1x Breach mkII
1 Gleive but never used it on the boss, you just don't have time to charge it. 
Cloak L1
Max shields
Near max dodge
No drones, no teleporter. 

One thing I nicked from a guide that no one mentioned here is, at the very end pump scrap into systems that need a damage buffer even if you can't power them, just spend the scrap on the next level and that will take damage when hit before the bars you are actually powering and using/that are vital.

Oh and...
No damage from boss L1. 
Took my time surgically taking out his systems and little biddy men, left about 3 alive. 

Second level, I don't think I took much damage at all, maybe 3-5. 

Third level, by far the easiest. Only 2 crew alive so one teleported over to me and he got stomped by my Rock crewman, that left one poor sod to try and juggle the entire boss ship by himself. It's quite pleasing to see him running around trying to repair shit. 
I nearly screwed up tho because he had a slither of health left and there were still 5 bars of hull on the enemy ship and he very, very nearly died before I got those bars, if he died I would apparently be in the shit with the boss AI taking over?

Didn't lose any crew on my ship and I didn't even see what my hull was in the end as it was nothing to be concerned about.

Most important augs to get (IMO) are the scrap recovery arm, or whatever it's called, and the long range sensors. It's all about grabbing as much salvage as you can.

The Stealth ship's tough but not impossible by any means. You do need a good start, though.

I completed a run with the Mantis layout B earlier. That ship is great fun. Four man Teleporter means loading up on Mantises and destroying crew. Top tip for the boss if you're attempting a boarding strategy: slaughter everyone except the guy manning the laser (immediately to the left of the cockpit). If you can take out the crew in the first stage, the rest should be a doddle as he can't repair anything so a boarding crew can get on board and take out shield unopposed. I say should, I wasn't able to take out the crew in stage one as the boss decided to hack my Teleporter. That was a highly frustrating battle. Once I was on to stage 2 I was golden.

Currently on sector 7 with the Slug Cruiser layout B. Not sure if I'll be in a position to take out the boss yet, but I've got one mantis boarding team and one rock plus the fire beam. Rock boarders plus fire weapons are awesome.

I'm also starting to like the charge laser/ion weapons. I've got one of each and they're proving great for battering through shields then pecking at systems.

And well done Panty.

Got to the boss on my 38th attempt. Got shafted.

Bastard Ancestry bastard Crystal Cruiser unlock quest bastard.

It's time I got some sleep.

Wahey! Ancestry and Crystal Cruiser unlocked!

I couldnae done it without you.

How many ships have you unlocked?

Finally beat the boss with the stealth ship. 

Was very rough going as my weapons were pretty poor, I had the two basic ones (small beam and dual laser) plus a flak cannon level I. Stealth weapons were a big help, maxed out shields and max cloak.  Flew through the final two sectors but it took AGES to penetrate the shields on the last three boss encounters.  Level 3 boss was eventually fun though, wiped out the two boarding parties which left the two fellas in the weapons room.  When I finally got through the shields the laser set fire to the shield room.  After that was a formality.

This game is tremendous, the iPad version is very well put together, but it's cost me many hours of sleep.

Found out today that it's not a good idea to destroy a ship without beaming back any crew you've sent over.

Ooh not seen one of those. Did the first phase of the boss today, I reckon I'll crack it soon.