Lioness of Cygnus Five — Alex Beecroft

In a Galaxy ruled under the righteous, iron grip of The Kingdom, Bryant Jones is a rare breed of rebel. Born on a planet of technological wonders, his world fell to The Kingdom, and their dictates, in a travesty of justice and might. His place was usurped and his mission of medical advancements was seen as perverted. Captured, tried and convicted of heinous crimes, Jones is on his way to a Penial Colony on the far reaches of the system... a colony he never intends to reach.
 
Once the Heroine of the Phoenix Nebula, Captain Aurora Campos has been brought low by scandal and judgement. Her trajectory towards the highest Military position in The Kingdom has been redirected to prison transport commander, an assignment meant to humble, shame and possibly silence her. Yet none can quiet the Lioness and she is determined to see this mission through, while protecting her crew and her charges both.
 
Neither knows what the future holds, or how soon their destiny's will collide, slamming truth and faith together in an epic battle that may shatter the very core of The Kingdom itself.

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Ever wished Stargate was a bit queerer? Or that Indiana Jones had a female hero, featured aliens and was set in space? This may be the book for you!

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Note, the next book in the series is Heart of Cygnus Five, but you might prefer to get the complete trilogy, imaginatively titled The Cygnus Five Trilogy, with all three books for a reduced price.