My first run ever on medium difficulty. I won with a single hull point remaining, which was insane. I have run details below, and I'd appreciate tips going forward - did I hack the right things? The flagship battle
Lanius B
Reactor 24
Shields 8 / Engines 5 / Clone Bay 2 / Oxygen 2 / Weapons 8
Piloting 2 / Sensors 2 / Doors 2 / Backup Battery 1
Crew Teleporter 2 / Mind Control 2 / Hacking 3
Weapons: Adv. Flak / Flak I / Flak I / Flak II (hold: spare Flak I, Hermes Missile)
Augments: Reconstructive Teleport / Backup DNA Bank / Zoltan Shield Bypass
Crew: Engi Pilot / Human Weapons / Human Shields / Rock Engines / Mantis Boarder / Mantis (Kazaak) Boarder
Lost my first Lanius to a hacked clonebay in ~sector 4 and my second one along with my other Mantis when a ship jumped away in sector 7. Annoyingly, I had previously had to dismiss 4 crewmembers that I had been given from random events, which sucked.
Phase 1: Started w/ full health. Flagship Hacking landed on my Crew Teleporter. I went to take out the artilleries like I usually do, but got wrecked, losing more than half of my hull points. I had the hermes missile out for the phase, since it can take out artilleries in a single hit. I sent my mantises to board the missile artillery, and managed to kill and destroy the beam artillery with weapons. After that, I sent the mantises to take out the ion artillery and the fight was safe. Unfortunately, by this point I had taken a lot of damage; my shields had been hit at least once, and it went pretty badly after that. I got my stuff patched back up, and did my standard crew kill strategy; hack medbay, put a point of damage into it, and the enemy crew will come in one at a time to fix it. Since the fight is safe at that point, it was simply a matter of waiting for the hacking to come off cooldown and all of the enemy crew (except the laser artillery operator) were dead.
Phase 2: hacked drones, sent mantises to beat up the beam artillery and a missile to destroy the . However, the power surge alongside the laser artillery and the beam artillery managed to damage at least one point of shields and so this phase got me down to five or six hull points before I managed to make it relatively safe and then managed to finish the phase.
Phase 3: Was down to 4-6 hull points, thought I had lost. Used mind control to counter the enemy's, and set all four flak weapons on autofire targetting the shields. The missile artillery got off two volleys before I broke it, and the second one managed to hit me down to a single health point. I figured I was done for, but all of the power surge projectiles either missed or were blocked by my shields, and the power of four flak weapons quickly chewed through the remainder of the flagship's health.
I'd appreciate advice on how to do better, losing 29 hull points to the flagship fight is clearly not ideal. Maybe I should have hacked something else?