I'm guessing the next update will be about finding the queen.
Petra is probably the vendor and the cabal that were monitoring the dreadnaught are the main enemy.
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Personally, the only way I see the Queen surviving that demolition is if The Nine had some part to it. [spoiler]I might have just opened Pandora's speculation box.[/spoiler]
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Well we know the cabal were there. They crashed one ship into the dreadnaught so it's possible they had a scout or something monitoring the situation. Capturing an enemy commander like the queen or at the very least getting to scrounge around their flagship would be a major priority for any military.