Yeah, the alliance/destroy ship sequence is worth 1.2 million exp per person, but it isn't critical to the game. One time, I just skipped that entirely, and there was no difference in the ending, or going to Ascension Peak. On the bright side, it also means you stay in good with the Templars (they become hostile when you free the prisoners). So just head on over to the Peak.
Nightowl2
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