Sentience

A new year brings new adventures. The USS Black Hawk, fully repaired and extensively refit following her near-fatal mission in the Convergence Zone, is launched from Gamma Command to perform a light shakedown cruise in order for her crew to become comfortable with the changes aboard the starship. Holographic interfaces and avatars, new technology, uniforms, and even procedures to help maintain safety aboard the legendary vessel.

However, the Golden Stars… the Consortium… the Dolmoqour… none of them could have ever prepared the crew for a set of perfect conditions and an ion storm, and the birth of a new Artificial Intelligence that sees the nearly nine hundred souls aboard as an invading virus.

For the full summary, see this wiki article.