The Discovery is still orbiting Pahvo. Admiral Terral orders Captain Lorca to retreat back into Federation space.
Lorca has no intention of leaving the defenseless lifeforms on Pahvo to the Klingons, so he purposely only uses warp to travel rather than the spore drive, allowing the Discovery to jump back to the defense of Pahvo when the Klingons arrive.
To give the ship an alibi, Lorca orders Lt. Stamets to have a complete workup done in
Burnham and Saru are working on how to solve the problem of the Klingon’s cloaking ability. They have an idea, but it requires sending a boarding party aboard a Klingon vessel to install sensors. It's workable, but it will take days to gather sufficient data about the ship.
Lorca goes to med bay to check on Stamets. Dr. Culber has found some adverse side effects happening in Stamets’ brain.
Lorca pulls Stamets aside. Lorca wants Stamets to make 133 micro-jumps to gather all of the information they need to plot the algorithm that will allow them to defeat the Klingons’ cloaking device. Stamets is doubtful that they’re even capable of using the ship that way, but Lorca is confident.
Lorca has also been tracking Stamets jumps. Stamets looks at Lorca’s data and realizes that it may have the secret to parallel dimensions and even time travel. Stamets agrees to make the jumps.
Lorca orders Tyler to put together an away team to board the Klingon Ship of the Dead. Tyler wants Burnham on the team. Lorca refuses, even when Burnham points out that she’s the only one who has been on the Klingon ship. Burnham is trying to figure out why Lorca is being so protective of her. Lorca finally agrees to let her go.
Culber equips Stamets with a device that lets him give treatment while Stamets is making jumps.
Lorca gives a speech to his crew, telling them how impressed he is with how far they’ve come. They receive the signal of a cloaked Klingon vessel entering the orbit of Pahvo and jump back to meet it.
The Klingon Ship of the Dead arrives in orbit around Pahvo. Kol orders the ship to decloak, open fire, kill the crew of the Discovery, take the secret weapon, and destroy the planet Pahvo and its transmitter.
The ship decloaks and Tyler’s boarding party beams aboard the ship. Lorca orders the Discovery crew to keep the Ship of the Dead busy.
Tyler and Burnham begin sneaking around the Ship of the Dead, placing their sensors. They place the first and keep moving. Burnham’s instruments sense a human’s life signs on board. Tyler doesn’t want to go off mission, but Burnham insists they search for the other human. They force open a door and find Admiral Cornwell inside with a pile of Klingon corpses. Tyler also spots L’Rell sitting among the dead. Tyler has a flashback to some kind of Klingon torture.
Burnham fires her phaser at L’Rell. Cornwell comes to and tells Burnham that Tyler is in shock and will be no further help to her. Burnham gives a phaser to Cornwell and tells both Cornwell and Tyler that she’ll be back when the mission is completed, that everyone is coming home.
The battle between the Discovery and the Ship fo the Dead is still ongoing. Burnham reaches the bridge, where she places the second vessel.
Lorca calls for black alert, hoping to convince the Klingon ship to cloak again. The Discovery’s jumps confound Kol and the Klingons. Discovery jumps and fires until the Ship of the Dead cloaks again. The sensors begin transmitting the cloaking frequency and the Discovery begins jumping again and again. Stamets’ pulse becomes dangerously high.
Cornwell tries to talk Tyler through his traumatic episode.
At 60 jumps, the job is starting to take its toll on Stamets. Culber tries to get Lorca to call it off. He refuses, and Culber applies some kind of treatment to Stamet through the device he gave him.
Kol receives reports of possible sabotage near the burial chamber. He orders the ship to warp. To stall him, Burnham opens fire. She comes face-to-face with Kol. She sees Kol gripping the Starfleet emblem that belonged to Captain Georgiou. He mocks her with it. She tells Kol that she was the one who killed T’Kuvma.
Klingons are at the door of the burial chamber. Cornwell prepares to defend herself with the phaser Burnham left. She hits one Klingon and tries to get Tyler to snap out of it and help her. When he’s reminded of Burnham, he finally comes to and deals with the other Klingon and then closes the door.
Kol thanks Burnham for what she did. The death of T’Kuvma allowed him to rise, and now bringing T’Kuvma’s assassin back will further earn the loyalty of T’Kuvma’s former followers. Burnham challenges Kol to combat. He accepts and tosses her a blade and they begin their duel.
The Discovery completes its jumps. Saru says he needs five minutes to calculate the cloaking algorithm. Lorca wonders why the Klingon ship isn’t firing at them now that they’ve stopped.
On the Ship of the Dead’s bridge, Kol and Burnham continue to fight.
Saru completes the algorithm. Tyler and Cornwell are beamed back to the Discovery and L’Rell grabs onto Tyler to go for the ride. Burnham retrieves Georgiou’s badge and is beamed back. Lorca orders the Discovery to open fire and the Klingon Ship of the Dead is destroyed.
Admiral Terral tells Lorca that Admiral Cornwell’s emergency medical ship has arrived at its destined space station. Terral also reports that cloaked Klingon ships are approaching Federation space. Terral orders the Discovery to Starbase 46, where Lorca will be awarded the Legion of Honor by Starfleet.
Burnham visits Tyler in his quarters. She asks him about his reaction to seeing L’Rell. Tyler says he thinks Burnham already knows. He says she’s the reason he’s had nightmares every night, but also that she’s the only reason he survived the Klingon prison. He encouraged L’Rell’s affection because he knew it was the only way he’d survive. Burnham comforts him. He says he’s found peace and they kiss.
Lorca finds Stamets and tells him about how Starfleet wanted to give him a medal, but he told them to give it to Stamets instead. Stamets offers to perform one more jump to make sure the Discovery and its crew are back to safety before the Klingons arrive. Lorca talks about what a new era this is going to be for Discovery, but Stamets clarifies that his jump home will be his final jump ever. He needs doctors to examine his condition and figure out what’s wrong with him. Lorca tells Stamets that he’s served Starfleet honorably.
Tyler has his nightmares of L’Rell again. He wakes up still on his couch next to a sleeping Burnham. He goes to the ship’s bridge to face L’Rell. He asks her what she did to him. L’Rell says she will never let them hurt him. The alert sounds, Tyler exits the brig.
Stamets prepares for his final jump, making plans to visit the opera on a moon near Starbase 46 with Culber. Lorca plots a course, but as the jump happens Stamets screams and his chamber ices over. Tilly reports the computers saying it was an incomplete navigation sequence. They pull Stamets out.
On the bridge, Saru is unable to determine their position, but there’s wreckage all around them.