So I seem to have discovered an annoying feature of the Deep Cover side quest. I found a pirate ship landed on a planet, killed everyone outside and inside, and took it. Arrived at New Atlantis and they scanned and found contraband. That set off the quest. I didn't want to get involved, so I went back to a save from before i got in the pilot seat. I found the contraband (on a table) and threw it off the ship . Went to New Atlantis and tthe same thing happened. Went back to an even older save where I'd only just killed the crew, and searched the hold - no screened hold. As best as I can guess, if you pick up the contraband then you are screwed, even if you then dump it outside the ship.
And yes, the combat is pants. Most annoyingly, because the take-off and arrival at systems are scripted events, you can find yourself getting bounced on arrival, and even hit before you can react. My (rebuilt) ship is a it slow and unmanoeuvrable, but it's got a fairly good shield and big offence, so getting splatted by a couple of level ten pirates as soon as the video ends is annoying.
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