I pick up the warheads but it still doesn't register as a completed mission objective? What am I doing wrong?
YOu need to go back home and escape with the warheads intact
shift+p pick up the warheads, get back home, drop the warheads (shift+r) fight, pick warheads up, and hyperspace to your new home. i just finished the level a hour ago.
You can successfully avoid losing the cargo if you avoid getting hit by missiles. This is rather difficult to pull off, however, and unless you are playing on the EASY difficulty setting I would recommend following the advice of Rogue15.
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Uriel Shadowstiehl
After you dock with the warheads, just stay in the hangar until Aeron hypers out, then dump all energy to engines and get out!