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.

Our Lower Deckers have trouble bonding with Ensign Jet Manhaver, who has been assigned Boimler’s bunk and shift duties. Meanwhile, we get a glimpse of Boimler’s life on the U.S.S. Titan, which is more intense than he thought it would be.

Assigned a special task by Dr. T'Ana, Tendi enlists Mariner for help. On the U.S.S. Cerritos, Rutherford is consumed by a bridge crew mystery.

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

Anomaly consolidation day on the U.S.S. Cerritos leaves the Lower Deckers with mixed emotions. Captain Freeman attempts to negotiate peace on the Pakled home world.

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.

A consultant arrives on the U.S.S. Cerritos to run drills that require the lower deckers and bridge crew to swap duties.

Boimler tries to find a friend from the bridge, while the crew of the USS Cerritos has free time during a long warp trip.

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