While the Cerritos escorts the decommissioned starship Voyager to Earth a dormant Delta Quadrant "macrovirus" is awakened. It combines with Borg technology and take control of the ship. Meanwhile, on the Cerritos, a stray Delta Quadrant flower petal causes a transporter accident that merges Dr. T'Ana and chief engineer Billups into one person, "T'illups".

Mariner vows to do anything she has too, in order to get demoted, while Rutherford tries to get promoted, but is outdone by Ensign Livik at every turn. Boimler moves to one disastrous room after the other.

Boimler leads his first away mission on an alien megastructure. Freeman puts her archaic technology Starfleet Academy training to go use while trying to fix a master computer.

Tendi is summoned back to Orion for a wedding. Rutherford and Boimler argue over who gets to water their bonsai plant. Captain Freeman must resolve a conflict she has with a Chalnoth, in order to a oscillating nebula.

Shortly after beaming a Betazoid delegation aboard the Cerritos, the crew starts acting strange. Provisional Lieutenant junior grade T'Lyn, wants to return to her old Vulcan ship but is unable to send her letter.

Grand Nagus Rom wants Ferenginar to join the Federation, for a price. Mariner and Boimler are assigned to update the tourist guide for Ferenginar. Tendi and Rutherford must pretend to be married, to review the Frengi s customs and discounts.

Badgey overrides a Drookmani ship and Badgey attacks the Cerritos. Meanwhile, Tendi and Boimler go to the Daystrom Institute to oversee Peanut Hamper's rehabilitation and to gather AGIMUS's alleged intelligence on the mysterious vessel.

Boimler, Mariner, Tendi, and Rutherford are trapped in a collapsed cave while on an away mission to study aggressively growing moss. With communications blocked, they await rescue and recount tales of previous experiences trapped in caves.

Captain Freeman assigns the Lower Deckers an overly safe mission to try and keep a self-destructive Mariner out of danger.

Mariner finds herself held as the hoped-for ally of the disgraced Nick Locarno, now a megalomaniacal insurrectionist armed with a rebel fleet and a destructively planet-reforming Genesis device.