In Perilous Flight — Aaron K. Redshaw

Having commandeered an alien vessel, Samuel and a small group of survivors from Earth take flight. But their destination is unknown by all but their alien ship's computer, and their fearful journey is troubled by an uneasy truce between the Technophiles and the Waldenese, dwindling supplies, and a mysterious sickness that seems more than a sickness.

Meanwhile on a planet far away, a race known as the Alachrens face the possibility of extinction unless they can relocate to a nearby world. Their only obstacle lies in a disagreement with the original terraformers who decide they don't want to share this new world, ushering them into a civil war that could determine the fate of everyone on their home planet.