The Alligence Subverter seems to work perfectly on a ship with a master computer. Even if its -only- got a Master Computer. I've tested this a few times.
Which brings up the question, how should this work.. if a ship has a Master Computer and a Crew (Useless in normal SE4, yes, but with mods not necessary) would the Master Computer render the ship (and its crew) safe from the Alligence Subverter? Or would it be assumed the crew disables the Master Computer?
Hmm, I just checked it again and it works as advertised - MC protects ship from AS.
Are you SURE you are running 1.84
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