"Choose Your Pain" starts off with fisheye lens camera angles and Michael's dreams, causing her to feel remorse for using Ripper the Giant Water Bear as a catalyst for the Discovery’s experimental spatial jumps.
Captain Loose Cannon Lorca is told by the Admiral that his crew needs to hide in the shadows for a while and not get shot out of the sky while they implement other ships with their spore based travel tech. Lorca, of course, vehemently disagrees, but when an admiral tells you to jump, you ask how high.
Tilly continues to be member of the crew with an emotional range bigger than a teaspoon. Over lunch with Michael, she suggests that with all of the free time Michael has on her hands, now would be a good time to put her big, underutilized brain to work processing her emotions.
In short order, Captain Questionable Ethics Lorca is revealed to have a photosensitivity problem with his eyes and is kidnapped by Klingons (not necessarily due to the aforementioned eye problem). This leaves Saru in charge of the Discovery, and he immediately begins plans for a rescue mission. Michael raises her doubts about using Ripper as their catalyst for spatial jumps, but Saru dismisses her out of hand and pushes forward with the rescue attempt.
Lorca wakes up aboard a Klingon prison vessel in the company of one Harcourt Fenton Mudd. This Harry Mudd- who once charmingly bought a moon for his beloved and now deviously and without an ounce of remorse chooses to pass off the pain of a beating from their Klingon captors to one of his fellow captives- is a touch more conniving than his previous incarnation.
Dream induced empathy proves to be one hell of a drug, as Michael drags Dr. Culber over to Lt. Stamets to convince him that using Ripper is not a sustainable solution. Stamets counters with the statement that using Ripper was her idea in the first place, and we are at a stalemate.
Lorca meets his fellow captive, a Lt. Ash Tyler of Starfleet, who has made it through seven months of Klingon torture of all sorts, as the captain of the Klingon vessel has taken a liking to him. Mudd makes an impassioned speech about how Starfleet regularly ruins the lives of their numerous, dirt-side contemporaries without a doubt and on a whim. He then proceeds to steal the food out of their (very injured) hands as repayment for the wrongs dealt onto him by Starfleet as a whole. Lorca gets brought to the ships captain, who tortures him with bright light in his sensitive eyes.
Stamets, Tilly, and Michael work together and discover that as long as they can find a willing co-pilot for the spores, Ripper need not be involved. Acting Captain Saru confronts them and demands that they hook Ripper back into the system so that they can continue the rescue mission.
Lorca reveals Mudd to have been working with their Klingon captors the entire time, and readily admits to having blown up his last command—killing the entire crew except, conveniently, himself—in order for them to avoid becoming PoWs on Klingon space.
With the Discovery's latest jump through space, Ripper waves a white flag and shrivels down into a protective hibernation. Saru quotes Vulcan logic, saying that the good of the crew is more important than the good of the possibly sentient Ripper.
Tyler and Lorca break out of their cell, proving that perhaps Klingons aren’t all they are cracked up to be if two unarmed and heavily injured humans can take them out. Mudd is left behind, because no one likes a turncoat, not even Captain Unpredictable Lorca. With two phasers set to kill, they make their way onto a smaller cruiser and get picked up by the Discovery.
We find out that Stamets used himself to produce the power needed for their spatial jump out of Klingon space. Saru admits to Michael his jealousy of her being Georgiou's second. Michael gifts Saru with the Georgiou ancestral telescope. With permission, Tilly and Michael release Ripper back into space, where it can live out its days not being used as a piece of machinery.
The episode ends with the moment we were all waiting for: Culber worrying over Stamets while he resignedly brushes his teeth. This cavity-inducing display of affection is only tempered at the last moment, when they leave the bathroom and Stamets's mirror reflection stays behind.