After the crew wakes up to solve an anomaly, the computer hologram orders them back to cryogenic sleep. The crew sees the power of their freedom and starts to question the order.
Bren is pricked by a device set for him by the Sentinel Corps, and when a recorded message is played, he discovers the military's true agenda for Deepwater, and their plans for him.
The Deepwater encounters another version of itself which is piloted by an older version of Reb. The crew realizes that Earth launched more than one Deepwater, and the members reflects on their own lives.
The crew of Deepwater encounters a drifting spacecraft who's only occupant is a 12 year old female child, who is wandering the corridors of her craft alone, and in a half trance.
The crew encounters a drifting lifepod, it's only occupant an unconscious female whose blood contains traces of an unusual chemistry. Upon waking, she elicits extreme emotional responses from each of the crew members.
Zak creates a cyber-neural transmitter to induce and control 'prexes' -- which creates dangerous and unforeseeable consequences -- including strange power surges that jeopardize Deepwater's shield integrity.
A computer virus hidden in Gen's main processing unit gives rise to The Mentor, who's agenda is to establish a Rex III colony of 'perfect' people, and destroying the remaining 98% of the gene samples stored in the Gene Bank.
The structure of Deepwater Black, and the lives of the crew, are threatened by the presence of a metal-chewing alien organism that covertly boards the ship.
The Deepwater encounters a distress call, that turns out to come from a former sweetheart of Reb on an habitable planet. She too is a clone from her former original that was brought there by her father.