So ... the endboss .... (endboss spoilers)

[Amaror]

So i just got an incredible lucky run with the kepler. In the final level i had this:
weapons:
Burst Laser II
Burst Laser II
Halberd Beam
I had a weapon preigniter, every shield upgrade, 50 evasion chance, cloaking device, 8 crew members ... and i still did not make it.
I know it's the endboss and its suppossed to be really difficult.
Why i am basically asking is: Did you guys find any way to repair yourself between the different stages? The repair shops from the beginning dissapeared and it seems just impossible to defeat this enemy 3 times (Actually i don't know if there's a third form, i died fighting the third form) without healing yourself.
I mean i was so upgraded that no other enemy even managed to damage me and i still did not make it.

[Postal]

Try to grab a hull repair drone on your next run if you can find one. That should keep your ship alive between battles.

Where I think your build was really lacking was the weapons. The burst lasers don't fire often enough to keep the shields suppressed, and the halberd beam is at its best when the shields are completely gone. Throw in a missile/bomb weapon so that you can take their missile bay down ASAP, which should cut down a lot on the hull damage getting past your shields.

In my opinion, the crew teleporter is probably still the best anti-boss strategy at the moment.

[curithwin]

If I were you I would have tried to go;

Halberd Beam, Burst Laser II or III and a Breach Bomb II. They miss less often and do not get hit by defence drones.

Try and get an Attack Drone II as well helps, even and Attack Drone I helps.

[Pentekont]

I had a huge problem with the boss as well. I tried lasers, missiles, drones, cloaking, maximum shields... and nothing...

Finally I was able to defeat him after I started using teleport lvl 3. With low cooldown and cloaking i was able to beam 2 team to the weapon sections and paralyze the boss. The weapon sections are unreachable so they cannot be repaired! This is the only way I was able to kill him.

[fall_ark]

We've got a similar thread not long ago:
Hints to beat the boss
Some of the replies can give you some insights

If you have Cloak and reasonably good shield+engine (which you have), it's very possible to suffer relatively few hull damage in the first two fights. What you really need is a way to penetrate the boss's 4 shield - your weapon loadout certainly lacks in this front, as the boss has a rather high evasion rate and lasers are not very well-suited to penetrate them.

Shutting down the boss's artillery is the first step to an "easy" win against him, so either missile/bomb first or teleport your crew to take them down. When you put down two of their main weapons, you're basically invulnerable from its attacks and can take your time whittling it down.

It's better to have Defense Drones in second and third form.

Time your Cloaking to evade the most dangerous weapons. Time your weapons to penetrate its shield (or power down your lasers and beams until you don't need to worry about the boss's missiles). Juggle power to achieve highest shield/evasion when threatening shots are coming, etc. etc.

[Amaror]

Thanks for all the answers.
I just realized it's not that difficult. I made the mistake of not taking out it's guns asap. Pretty strange since i always done that with other ships, but my brain must have just got a blackout or something.
And the second time around i had a breach missile, instead of the beam. God, that was really helpfull.
So i beat him now, i am off unlocking more ships...

[Maze1125]

A teleport squad makes the final boss your bitch. As each of its weapons has only one guy defending it and they're cut off from any support.