Enemy Within by Marcella Burnard

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Blurb:

After a stint in an alien prison, Captain Ari Rose wonders why she even bothered to survive. Stripped of her command and banished to her father's scientific expedition to finish a Ph.D. she doesn't want, Ari never planned to languish quietly behind a desk. She wasn't built for it, either. But when pirates commandeer her father's ship, Ari once again becomes a prisoner.