Burnham dreams of being alone on the Discovery and activating the spore drive using herself in place of the tardigrade creature, Ripper.
The agony wakes her. Tilly snores.
She consults with Dr. Culber, explaining that despite the creature's regenerative powers, it is suffering every time the Discovery uses it to navigate the spore drive. It is now sluggish and depressed. He agrees to run some tests.
Lorca meets with Starfleet Command who want the spore drive duplicated on other ships down to the tardigrade navigation. Until they are able to obtain more, they want Discovery to pull back on using the spore drive for its missions, citing concern that the missions are taxing the only spore drive in the fleet. Lorca wants the Discovery to be front and centre, winning battles in decisive victories. He is ordered to reign in spore drive use in case the Klingons identify the Discovery as the key ship in the victories.
Tilly and Burnham discuss her current state of mind. Burnham can't understand how she can be stressed since she has never been less busy on a job. Tilly points out that she now has the time to process what she's actually doing and Burnham doesn't like it.
Lorca and Cornwell confer together after the strategy meeting has adjourned. She reprimands him for conscripting Burnham onto his crew since she is seen by many as the cause of the Klingon war. She sees this as bad for morale. He says that the powers he was given when he accepted command means he'll do whatever he pleases to win the war.
On the way back to Discovery, Lorca's shuttle is attacked and a Klingon battle cruiser uses a tractor beam to capture the shuttle. In the boarding of the shuttle, the pilot is killed, Lorca is identified and taken.
Admiral Cornwell contacts Saru, now acting captain, with the information of Lorca's capture. She orders him to rescue Lorca before the Klingons can extract information about the propulsion system out of him.
Burnham comes aboard the bridge to speak to Lorca and is concerned when she hears Saru say that the ship will be making multiple spore drive jumps. She voices her concerns about the effects on the tardigrade but Saru convinces her to focus on the rescue until she has proof that they are harming the creature. After he dismisses her, he tries to get the computer to run a protocol to gauge his ability as acting captain because Burnham makes him question himself. The computer suggests he eliminate Burnham.
Lorca awakens to find Harry Mudd standing over him and finds out that they are aboard a Klingon prison ship. Lorca notices another Starfleet officer in the corner. Klingons enter and demand that they "Choose Your Pain". Mudd points to the man in the corner. The Klingons drag him into the middle of the cell and beat him badly. Mudd explains it is how the Klingons keep the prisoners from bonding since they constantly choose between taking a beating themselves or offering up a cell mate. Mudd has no bruises, Lorca notes.
Burnham and Dr. Culber approach Stamets about the tardigrade's deteriorating state. Stamets sends Culber away and tells Burnham that this is her fault and it is up to her to fix it.
On Klingon vessel, Lorca meets Ash Tyler who claims to be a survivor of the Battle of the Binary Stars, from the U.S.S. Yaegar. Lorca accuses him of being a liar, that no one survives Klingon torture for seven months. Tyler explains that the captain of the vessel has taken a liking to him. He estimates the ship's complement to be 30 or 40 but he has no idea how they might escape. Lorca says his ship could rescue them if he could just get a signal out.
Mudd's pet arachnid steals Tyler's cracker and Lorca questions the wisdom of stealing from cellmates who might choose his pain. Mudd airs his grievances against Starfleet and accuses them of arrogance which caused the war. Klingons enter and take Lorca out.
Stamets discusses with Tilly and Burnham how they can find a replacement for the tardigrade's navigation ability. They realize they need to integrate the mycelium DNA into a sentient living organism that understands its role in navigating the ship.
Lorca is set up for torture. His torturer has excellent English, descended from spies who valued language. They know that he is photosensitive and use that to torture him. He manages to incite her to hit him when he taunts her with the knowledge that she is carrying on an affair with Tyler.
Saru is about to take the Discovery through jumps to rescue Lorca but Stamets has taken the spore drive off-line. Stamets, Tilly, and Burnham are discussing viable substitute species for the tardigrade when Saru storms in and accuses Burnham of insubordination. He orders Stamets to bring the drive on line and orders Burnham to confine herself to quarters.
Lorca is throw back in to the prison cell where he immediately de-bugs the arachnid, Stewart, and explains that Mudd has been feeding the Klingons intel from other prisoners in the cell. Lorca had been planting information since regaining consciousness and when he was tortured, he heard his own words come back to him.
When Tyler tells Mudd that they will choose his pain, Mudd reveals that Lorca escaped the destruction of his last command. Lorca corrects him in that he didn't abandon his crew, he blew them up to save them from being taken by the Klingons.
Saru orders a Discovery jump but it sends the tardigrade into a survival state, basically unresponsive. Saru wants them to force it to comply and Dr. Culber refuses to be a part of it. Stamets states that he will follow the orders.
Lorca and Tyler manage to subdue the Klingons when they come the choose the pain. They leave Mudd behind in the cell. Tyler tells Lorca to leave him behind, because he is slowing him down. Lorca swears he'll come back for him. The Klingon captain tries to recapture Tyler but he fights back and beats her down. When another Klingon tries to intervene, Lorca returns and disintegrates him. A ricochet shot hits the Klingon captain, knocking her down and Tyler and Lorca make a break for it.
They steal a raider but are pursued by the Klingons. As they approach the Discovery, Saru notices that erratic flight pattern and realizes that the lead raider is being pursued. They hail it and make contact with Lorca. They beam Tyler and Lorca out just as the Klingon raiders destroy their escape vessel.
Lorca orders a jump and Saru confirms with Stamets that the ship can make the jump to safety. Once they re-emerge, he congratulates Stamets but there is no response. The computer reports that Stamets' vital signs are dangerously low and the bridge crew rush to the lab where they find Stamets lying on the floor of the spore chamber, having injected himself with the tardigrade DNA and navigated the system himself. As Saru checks for a pulse, Stamets revives and is hysterically happy when it is confirmed that his stunt worked.
Saru enters Burnham's quarters to update her on Lorca's rescue. He confesses that he is angry and jealous of Burnham because she got to be Georgiou's first officer and he didn't. She gives him Georgiou's telescope. He accepts and orders her to save the tardigrade's life. She and Tilly release the tardigrade by airlocking it into space and it reanimates and leaps away using the mycelium network.
Stamets and Culber are preparing for bed, Culber still checking Stamets over for injury from the jump. Stamets reassures him that he feels fine but when he walks away from the mirror, his reflection lingers for some time before walking away.