Basic strat is to ensure that your weapons are firing to do most affect. Having auto fire on is actually bad in many circumstances. So for the boss I will target shields with missiles/bombs, and then target cloack/drones (first battle or second battle) with energy weapons. I cant remember what the 3 rd battle has as its skill so cant remember what to target.
Example of optimising firing rates is to have energy weapons only fire when the shields are down so they can damage the hull. Fire ion weapons before other energy weapons, because it will always do some hinky shit to the shileds, then you can quickly change the focus of the other eneergy weapons to take out other targets. Having a beam weapon is pretty good cos you can damage multiple systems at once, but unless you can consistantly keep their shields down, a beam weapon will generally make u weaker because its a weapon slot that isnt doing anything.
On the bose target the inner left weapon with all your damage, it's the strongest, and then slowly kill the rest of the weapons, you can kill shields but the weapon is really strong.
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