If I understand the episode correctly, Rush orchestrated the mutiny against Young because he knew the aliens had implanted a tracking device on him, and Rush was afraid Young would get rid of him because at least then Young would have had a good reason. Rush took advantage of Wray's distrust of Young and used her to lead the civilian personnel in the mutiny. Rush knew he needed the shields to resist the aliens' attacks when they did arrive, and presumably without Young over his shoulder he would have the time he needs to find a way to defeat the aliens when the Destiny got back into FTL after the attack.
Rush is indeed manipulative.
Rush is indeed manipulative.
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