Captain Lorca is called to a starbase where Admiral Cornwell orders him to limit the use of the spore drive of the Discovery, in order not to risk losing the only prototype. On the way back to his ship, Lorca's shuttle is boarded by the Klingons, and his pilot is killed. Lorca is taken to a prison cell with the criminal Harry Mudd and Starfleet Lieutenant Ash Tyler.
On the Discovery, Michael Burnham is concerned that the condition of the tardigrade deteriorates with each jump. Acting Captain Saru, however, orders her to carry on regardless, in order to find the missing captain. Burnham convinces Stamets to work out an alternative solution, incorporating DNA of the tardigrade to another living organism, such as a human. When Saru notices that the spore drive is down, he confines Burnham to her quarters and tells Stamets to activate the drive again. After jumping to the position of the Klingon prisoner transport, deep in Klingon space, the tardigrade's condition is so bad that the creature goes into stasis.
Meanwhile, on the Klingon vessel, Lorca finds out that Mudd has been spying on the Starfleet officers for the Klingons. When the guards appear again, to take one prisoner to be tortured, Lorca and Ash attack them. They manage to escape from the Klingon vessel in a raider. Saru recognizes that one of the raiders approaching the Discovery is being pursued by the other Klingon ships, and he arranges for Lorca and Ash to be beamed out. He then orders the jump back into Federation territory. Since the tardigrade is disabled, Stamets gave himself an injection of its DNA and performed the jump in its place. Saru orders Burnham to help the supposedly sentient tardigrade, whereupon Burnham decides to release the creature into freedom.