How did I defeat the aliens? Christ, that was ages ago. Erm, well, hang on (he goes and loads up EV with GS and the appropriate pilot file)... I was using a rebel destroyer - do the rebel missions available to you, and they'll make sure you have access to the destroyer before you engage the alien - with many mods - shield capacitors, all armour upgrades available, maxxed out the proton turrets, and because you're fighting the aliens, fit fixed as many guns as possible. In theory, neutron cannons should help no end, but their range isn't enough for my tactic, so I just used as many proton cannons as possible. What I did was circle the cruiser, using the autopilot button when necessary to bring my ship to bear to bring the guns round to the target. I also drew the pesky fighters away from the cruiser before returning, and let them shoot as many seeker drones as possible, because they really are annoying. Then do wide circles around the cruiser, and watch for the beam - do not, under ANY circumstances, allow them to shoot you with the beam, it drains your shield at a prodigious rate - until you defeat it. The annoying thing is having to break away to avoid the fighters, and so the cruiser recharges. It took me MANY times to finish that mission, and when i finally did my destroyer had 5% armour left. It's worthwhile, the later missions are excellent. I find that the destroyer's speed and manoeveravility help no end in the battle, but you'll need to keep an eye on the radar to check where the fighters are, they like to doiuble-team you so their beams combine to take down your shields super-quick.
Godspeed and good-hunting. Dismissed!
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"This lady needs to be taken to a hospital immediately"
"A hospital, what is it?"
"It's a big building with patients in, but that's not important right now"