Approximately three months after the events of the season one finale, the U.S.S. Cerritos is dispatched on a mission where it ends up in a sci-fi event resulting in "strange energy," which Commander Ransom inadvertently absorbs.

The U.S.S. Cerritos is dispatched to a planet to investigate an unexplained sighting of a dangerous Mugato.

Mariner and Boimler are stranded on an uninhabited planet with a sentient computer. On the Cerritos, Lt. Commander Billups must prove his engineering abilities to an old adversary.

In the season two finale, the U.S.S. Cerritos is tasked to aid another class starship on a first contact mission.

Mariner enlists her friends on a rogue mission to exonerate her mother, as Captain Freeman faces a military tribunal for the destruction of Pakled Planet.

Mariner, Boimler and Tendi clash with their arch-rivals: Delta Shift. The Cerritos engineers go on mandatory relaxation leave.

A wayward Starfleet ensign struggles to find a path to redemption.

The Cerritos crew must prove their worth in a mission race.

The Cerritos ensigns must assist a caretaker on the voyage of a historically significant starship.