Pilot Archive

Once you've destroyed the fighters, target the transport and use the ' ] ' key to target its engines or reactor. Shoot away and, once you've ploughed through the shields, you'll get a message informing you that the target is disabled.

On an aside, using the ability to target specific components to disable your targets is a good way to get some breathing space in those situations where you find yourself mixing it up with a multiple waves of targets a tier ormore higher than you. Disable one ship in a wave and, while it will eventually self destruct, the next wave won't appear until it does.