100% Boarding Strategy-Not for use in Hard Mode
Systems required: Cloak, teleporter, clone bay (recommended) and hacking (optional)
Upgrades: Level 3-4 shields, level 2-3 teleporter, level 1 cloak (its recharge will come fast enough for power surges), level 4-5 engine (for 100%+ cloak dodge rate)
Preferred weapons: Ion burst mk II or ion bomb (with weapon pre-igniter) for zoltan shield), high-dps weapon as a finisher (beam, flak mk II, chain vulcan, etc.)
Preferred Augmentations: weapon pre-igniter, automated reloader (if you have good burst damage weapons); reverse ion field (for the boss ion, although it becomes obsolete after the first stage); reconstructive teleport, zoltan shield bypass (for boarding)
Preferred Crew: 4-5 mantis/crystal/lanius/rock (in terms of effectiveness; mantis will take out the missles, crystal can be used to prevent crew from going into the medbay after the missiles are down, and lanius and rock are simply other good boarders)
Important: If the boss hacks any crucial system, be prepared to jump out.
As soon as the boss comes out of its cloak, send two boarders into the triple leto launcher. Cloak yourself (any level cloak will do for this stage) when the missiles come at you. When your teleporter's CD is up, teleport into the ion blaster. Retrieve your crew from the missile launcher once it's destroyed and teleport them into the beam weapon, then teleport your crew back from both weapons when they're destroyed. Now, to destroy the rest of the ship's crew (leave the triple laser man alive, or else you will face the wrath of the AI!) Do not fire any hull-damaging weapons as you don't want to leave your crew on the flagship as it jumps away!
Teleport your crew into the medbay. When the ship's men come to fight, send your hacking drone at the medbay and hack it. This ensures that the enemy crew will have a tough time trying to escape your crew and will not fight them in the process, saving your crew from damage.
An alternate hacking strategy is to hack the doors subsystem and activate the hack when enemy crew is at low hp and you don't want them to escape.
Some ships can only hold 2 additional systems, or your luck at shops has run out. Although this can make things difficult, killing the crew in the main part of the ship is still possible.
One method is to destroy the medbay with weapons (make sure you don't reduce the hull to 0 doing so), then teleporting into the medbay as to prevent the enemy crew from repairing it. Clone bay is helpful here as you will be dealing with 2 v 4 situations while trying to teleport additional forces in.
The other method is to send 4 mantis into the shield room (in 2 waves of 2 or all at once using the crystal/mantis ship). If done correctly, only one enemy crewmember will enter the room at a time and will not be able to escape as the mantis's DPS is too high.
After the enemy crew has been killed (with the exclusion of the triple laser gunner), give them the gift of free XP by destroying the ship's systems (excluding oxygen and the triple laser weapon). Keep in mind that destroying a system will deal 1 hull damage. Then, use whatever weapons you wish (basic laser, mini beam, etc) to destroy the helpless 0-evasion ship. I sound like a broken record, but don't kill the triple laser guy!
Now that the enemy has no crew in its main section, your crew can destroy systems uncontested. Your first boarding move should be into their drones system or missile weapon. The first point of damage to the drone system will disable their boarding drone. Cloak (lv 1) whenever the triple laser is firing with the drone surge; lvl 3-4 shields should hold up the power surge by itself (unless the boss beam is still up). Destroy shields and piloting only if you're desperate to destroy this stage; if not, you can destroy all the other systems (except oxygen and the triple laser). Again, use whatever you want to get rid of the hull when you feel like you're done.
Cloak every power surge except the regen zoltan shield ones.
-With zoltan shield bypass:
Board aggressively, trying to disable the missile launcher and the mind control. Deal whatever dps you can and try to beat the boss! Tip: you can leave crew on board the flagship at the stage; it's the last fight anyway!
-Withough zoltan shield bypass:
Use ion weapons if you have them (they deal double damage to zoltan shields). any salvo weapon is useful as you will want to get rid of the shield ASAP. Teleport into whatever you want (except the two aforementioned systems) and try to deal whatever damage you can.
Why is cloaking essential to this strategy?
Crew takes a much longer time to damage systems than weapons, and you will have to wait for extended periods of time waiting it out.
Congratulations! You have beaten the rebel flagship!