Parallax, Halcyone Space, book 4

After a reckless young computer programmer resurrects the damaged AI on a long dormant freighter, she and her accidental crew blunder into a galactic conspiracy forty years in the making.

Welcome to Halcyone Space:

PARALLAX (Book 4)
In the aftermath of the Ferryman's death and Lieutenant Commander Gutierrez's injuries, Ithaka has lost its most loyal protectors. The Commonwealth is coming dangerously close to discovering the lost planet's location and crushing its lingering rebellion. As Ro and her crew fall under suspicion of harboring Ithaka's secrets, they race to unlock Ro's father's trove of encrypted data in order to find leverage against the rebellion's enemies.
But knowledge brings new threats and Halcyone's crew is drawn more deeply into a conspiracy that threatens to destroy Ithaka and reignite a galactic war when they uncover the hidden power brokers who have been quietly manipulating the Commonwealth for decades.