After some dialouge, my hull gets repaired. This is the final sector and I will have to face the Rebel Flagship. He has 3 stages. I will explain these in greater detail after doing some last preparations.
I have to get to the base, so I move to this beacon.
I try to avoid fighting this enemy so I hack its drone control. The weapons can't pierce my shields.
My teleporter and shields get hit because my shields get overwhelmed by the high amount of drones.
After my FTL drive is ready, I jump to the Repair beacon.
My hull gets fully repaired and I get some nice ressources.
I fix the teleporter, shields and doors which have been hit,
heal my crew members
I now do some upgrades on my ship.
I upgraded my shields to 3 and my engines up to 45% evasion. My weapons have enough energy to run all 4 weapons.
I jump to the location of the Rebel Flagship.
This is the final fight. Stage 1 consists of the Rebel Flagship shooting all of his 4 threatening weapons.
He cloaks at the beginning of the fight.
He hacks my hacking system, this allows me to ignore his hacking system because it will do no harm to my engines/weapons/shields.
I teleport my boarding crew into the missile room, the advantage of that is that once that guy is dead there won't be anyone manning those guns in future stages, making the boss easier.
I then attack their laser weapons, ignore the Ion weapon (very left) and the beam weapon (very right) for now because if you disabled the missiles and laser weapons in this stage he can't do any harm.
He hits my drone control so I move my humans in to repair it immediately.
He will cloak again, but in the meantime my boarding crew keeps on hitting the missile weapon.
After the missiles launcher is destroyed, I teleport my crew back
and heal them up.
I destroyed the beam gun by shooting at it and now board the Ion weapon.
I teleport my crew back once again.
I then destroy the laser gun, the ship is now not able to attack in any way.
I then attack the shields, I don't need to be careful since every weapon is disabled.
That was the 1st (and probably easiest) stage.
I do a reactor upgrade with the little scrap I have
and jump to the Rebel Flagship's next location.
The second phase, note that the Ion weapon is cut off the ship and there is noone manning the guns. The boss is focused on drones in this stage so disabling the drone control is crucial.
I teleport my boarding crew immediately into the missiles launcher room while waiting for my Charge Ion to get additional charges. I also disabled the medbay and the hacking system and put that energy into the Defense Drone. Reason behind that is that the Defense Drone I will shoot down boarding drones which are very hard to deal with. They create a breach in the room they crashed into, have 150 health and are strong so having the Defense Drone I is very useful here.
I teleport my crew back and fired a few shots with the Ion weapons to reduce the shields. The missile launcher is destroyed so I do not have to worry about that.
I focus my efforts on the drone control because the ship uses power surge drones. This is a short period of time where the Flagship sends a very high amount of drones to attack my ship.
I keep firing on the drone control and teleport my crew into the laser weapon room.
After taking care of the laser weapon, I teleport them back.
I now focus on the drone control since the enemy has only a small chance to inflict damage on my ship.
I killed off another crew member while he was trying to repair the drone system
and finish it off by keep attacking it.
I use the scrap to do another reactor upgrade
and jump to the beacon the Flagship will go to.
I fire all of my weapons straight away to destroy the Zoltan shield as soon as possible. Meanwhile I keep my mind controlled crew member busy. This stage is dangerous because it either shoots 8 heavy laser shots at once or regenerates its Zoltan shield.
I continue to fire my weapons at the Zoltan shield. He tries to board me and I keep the mind controlled crew member busy.
My teleporter is on fire and my doors are broken.
My piloting system is also damaged.
I take a lot of damage and can't deal with this current situation so
I jump away. I have now time to take care of the fire, the teleporter etc.
After I repaired everything and healed everyone
I wait because my current location is the one the Flagship will jump to.
My crew member is mind controlled.
I shoot everything to disable Zoltan shield. I also activate the Defense Drone I to shoot down some missiles.
I send in a crew member to keep the mind controlled crew member busy. After I took out the Zoltan shield, I teleport my boarding crew into the missile launcher room.
The crew member keeping the mind controlled human is low on health so I send him to the medbay. My engines have been damaged, but only a bit and my hacking module is destroyed and on fire.
I send in both engineers to take care of the hacking system. The missile weapon is also disabled.
After extinguishing the fire, I send the engineers back. There is no need to repair the hacking module since I'm not using it. My engineer in the weapons system is mind controlled which is quite a big deal.
This situation looks bad, my teleporter is damaged, the piloting system is on fire and destroyed resulting in 0% evasion and the weapons system can't be repaired until the mind controlled engi comes back to his senses. On top of that, my hull is pretty low.
The engi finally regains control and barely survives. I send him to the medbay immediately. The fire in the piloting system has been taken care of.
I keep on shooting the mind control and try to repair the teleporter.
I send in the Mantis and the human who repaired the teleporter into the laser weapons room to disable it.
The other human, the engi and the slug are now fixing the breach. I open every door inside to spread the oxygen.
The weapons are fully fixed and I keep the focus on the mind control.
After finally destroying the lasers, I teleport both back. My pilot has gotten mind controlled though.
This is a huge mistake, but I tried to take down the mind control. I killed every human so the AI takes over which is more difficult to deal with.
It charges a new Zoltan shield which I try to destroy. The pilot has come back to his senses and I move the slug towards the teleporter.
I heal the engineers a bit because I am afraid of them dying by a stray shot.
The AI can repair the weapons, so I teleport my boarding crew into the missiles room again because it is currently the biggest threat.
After doing so, I teleport them back. Meanwhile I charged my weapons and I am waiting for the Charge Ion to get its 3rd charge.
I have a lot of problems to get through the shields because it evades a lot of my shots.
And again I missed a lot of my shots.
I send in my boarding crew out of desperation because my hull has currently only 3 HP. I send them into the engines and try to do as much damage as I can.
With the broken engines I am finally able to get through the shields
and destroy the Rebel Flagship.
I beat the game, unfortunately I lost my boarding crew but it was all for the greater good.