- While on a mission, Lorca is captured by the Klingons and unexpectedly finds himself in the company of prisoner of war Starfleet Lieutenant Ash Tyler and notorious criminal Harry Mudd.
- Burnham believes that the Ripper undergoes intense physical pain during the spore drive jumps. She consults ship medical officer Culber and says that Ripper has regenerative abilities, but has been very sluggish for the last 48 hours.
After a month of successful operations, Lorca is ordered to protect the spore drive until it can be replicated for other Starfleet ships. But the Starfleet needs more Tardigrades to make the spore drive operational on other ships. Lorca is told by Admiral Cornwell that until they find more, he should not be taxing the only Tardigrade they have in captivity. Cornwell says that Klingons may have gotten wind of his new propulsion system. Cornwell orders Lorca to stop using the spore drive unless authorized by Starfleet.
As he returns to the Discovery, Lorca is taken captive by a group of Klingons led by L'Rell. Saru is now acting captain of the Discovery. Saru starts to search for Lorca using the ship's resources. Saru wants to make multiple jumps using the spore drive, to locate Lorca within Klingon territory. Burnham updates Saru regarding her concerns about the Ripper's health. Saru dismisses her concerns as the priority is to find Lorca.
Burnham has grown concerned by the toll that the drive has taken on Ripper. Along with Stamets' partner, medical officer Hugh Culber (Wilson Cruz), Burnham convinces Stamets to find an alternative to run the drive. Culber says that there is a chance that they lose the Ripper, and hence the spore drive.
Stamets explains how the root of the fungus makes the Mycelial network acts as a matrix that serves as an intergalactic freeway system. The Tardigrade's unique genetic makeup allows it to navigate the network because of its symbiotic relationship with the Mycelial spores. When Ripper borrows DNA from the Mycelium, it is granted an all-access travel pass around the galaxy. Tilly suggests building a virtual Ripper, thereby tricking the Mycelium into thinking it is communicating with the real thing. Stamets replies that he already tried that; it only allowed for small jumps. He knows why now - the spores and the drive were functioning at only a fraction of their capacity until they introduced a living co-pilot. Stamets announces that all they have to do to relieve Ripper is introduce the same sequence into a compatible host, one that understands its role in the process and does so willingly.
The team cannot find a organic host that is compatible with Tardigrade DNA. Saru wants to use the spore drive, but find it offline. Saru blames Burnham for endangering Lorca's life as she did for Georgiou. Burnham argues that human host is the most compatible with Tardigrade, but Saru forbids any human experiments. Saru orders Stamets to use the Tardigrade to jump into Klingon space to a battle cruiser where he believes Lorca has been imprisoned. After this jump, the Tardigrade goes into survival mode, sheds all of its body water, curls up into a ball and goes into hibernation. Saru asks Culber to comply the creature to cooperate, but Culber refuses.
Lorca is imprisoned with captured Starfleet officer Ash Tyler (Shazad Latif) and human criminal Harry Mudd (Rainn Wilson). Mudd escapes torture by Klingons by accepting their offer of getting his cellmates receive the torture instead of him (this is technique by the Klingons to keep the prisoners from bonding with each other). Ash says that he was captured at the battle of the binaries. Lorca cannot believe that Ash survived torture for 7 months, and Ash says that the Klingon captain L'Rell has taken a liking to him. Ash knows there are 30-40 Klingon on the ship. Lorca is tortured by L'Rell, who wants to learn the secret behind Discovery's new form of travel. Lorca finds that Mudd is a mole for the Klingons and has been feeding them intel on every prisoner in exchange for his survival. In discussions Lorca reveals that he killed his entire crew during an earlier battle to spare them from the Klingons' torture but escaped himself.
Lorca and Tyler escape before the Klingons can learn anything about it. Lorca leaves Mudd behind for selling them out. Lorca singes L'Rell's face before escaping in a Klingon shuttle. Lorca flies the stolen shuttle away from the battle cruiser, but is pursued by Klingon raiders. Saru observes the escape, and is able to recognize that the lead shuttle is being hunted. He initiates communication and finds Lorca. Saru beams Lorca and Tyler to the Discovery.
For the final jump needed to escape the Klingons, with Lorca and Tyler on-board, Stamets connects to the spore drive himself as the human host using Ripper's DNA. After the jump, Stamets goes into distress, but revives shortly thereafter. Burnham mends bridges with Saru and gives him Georgiou's telescope. Saru asks Burnham to release the Tardigrade. The Ripper revives in deep space and flies away. Later, Burnham frees Ripper while Stamets' reflection in a mirror does not walk away when he does.
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