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Will I still have to face the later forms? If I do have to face the later forms, will I lose my boarding party when it escapes?

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Well, it turns out killing ALL the crew is a really bad idea. –  Fambida Sep 24 '12 at 4:00
    
What happens when you do? I've killed all crew once a few seconds before defeating the final form, so I couldn't really tell what difference it made. –  kotekzot Sep 24 '12 at 7:58
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@kotekzot It activated an AI which repaired every system at the same time. So all the isolated weapons which I'd disabled came back. –  Fambida Sep 24 '12 at 13:21
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AI auto-repairs systems, but at a much slower rate. If you can keep up the damage, it can be easier to deal with (but one or two enemy crew will be easier still). –  Samthere Sep 27 '12 at 12:52
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up vote 19 down vote accepted

Killing the crew in first phase means they won't be there in the next two, same if you kill them in second phase: they won't be there in the final, so killing them can be a good tactic as they may trouble you later.

If you kill them all you won't win that phase or overall, instead the ship will go into auto-pilot and will slowly repair all its systems much like the auto-assault scout drones in earlier sectors. It's best to leave one enemy crew alive, maybe the isolated guy on their laser tri-shot; because fighting an AI Boss is much harder than fighting a single panicky engineer.

When the ship flees to its next phase your boarding crew will be killed if they are still on board, same if you destroy it completely with your crew on board, meaning their noble sacrifice won't go down in the credits.

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Keep in mind that the flagship won't flee just from losing its crew. It can only be defeated by hull damage. This means your boarders can be safely beamed back before you finish the job. –  Samthere Sep 27 '12 at 12:54
    
Keep also in mind that if the enemy flagship has crew-members, a system needs a crew member in it in order to repair it. However, if the flagship is running on auto-pilot, it can repair any system (including the weapons only reachable with the teleporter), so it may be a good idea keeping a few enemy crew members in the beginning to prevent the enemy ship from auto-repairing any system it wants. –  IQAndreas Dec 21 '13 at 2:53
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