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After I did the Rebel alien missions, and could buy the Rebel Cruiser, I still couldn't get the Manta, Rebel Destroyer, or Rebel Cruiser as an escort. It's the same with the Confeds. How do I get the Rebel ships as escorts?
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You just have to get lucky when boarding those ships, and hitting "Capture Ship." There is no sure-fire way to get a capital ship escort.
If you have a lot of money you can do this:
In your big ship, disable a small ship like a Clipper, Courier, Shuttlecraft, Scoutship, etc.
Board it, hit Capture.
Hit "Use as my Ship." Yes it sounds crazy, but...
Your old ship will be retained as an escort (unless you already have the max amount of escorts).
Proceed to Palshife/Luna and buy a new ship.
There, you have a capital ship escort. Sure you lose money but once you get tribute of 100,000 credits a day or so it doesn't matter. Hope this helps.
Thank you for your advice Smashman, I really think this will help.