Mark is taken down in a Prolethean shoot-out and Sarah must step in to help. But as Sarah gathers intel that puts her on the trail of the original Castor DNA, a familiar foe is not far behind. While Helena continues to toil in a faraway military compound, it is ultimately Sarah’s fate that will hang in the balance as she tries to save her sister. Meanwhile, Gracie is cast out from the Prolethean fold, and Alison and Donnie come face-to-face with unhappy drug lord, Jason Kellerman.
Bonnie Johanssen hunts Sarah through Willard Finch's farm, but Sarah escapes, and helps Mark get away despite his wounds.
Bonnie takes Gracie to the house where the Johanssen family is now, the home of Jonah Appleyard, who took the family in after the fire. Jonah welcomes Gracie, largely by the promise of the child Gracie is carrying.
At the army base, Helena bashes herself and makes enough noise to get the guards to come control her; she is bloodied enough that they take her to the infirmary, where guards hold her down as Virginia Coady injects a sedative.
Once they leave her alone, Helena's scorpion tells her hurry, the drugs will soon set in. She gets up and starts to explore the infirmary, and the base, before she really gets sedated. She finds another medical area, where there's what looks like another Castor, very sick, and immobilized in a chair. Close to collapse, Helena makes it back to where she started in the infirmary, in time for the guards to come to take her back to her cell.
Alison and Cosima discuss things by phone: Cosima is doing better due to the stem cell treatment, but the Castor boys are seriously sick and need some sort of treatment, which the Castor original would help with. Alison hangs up as Donnie runs in, he thinks he was being followed by car, so they plan to get all the incriminating evidence out of the house to a storage locker.
Sarah gets Mark to an empty house, and he has one bullet still in his leg, he'll need her help to get it out, but in exchange she wants answers. She gets the bullet out, and asks where Helena is, but Mark has been out in the field a long time, and their headquarters moves, they could be anywhere now. He says they thought Henrik Johanssen had Castor samples, but Mark had searched and hadn't found anything.
Donnie and Alison are carrying plastic tubs of soap and drugs outside, and find a stranger, Lionel, sitting there; Donnie says he's the one who was following him. Lionel works for Ramon's supplier, and the drugs Alison bought weren't Ramon's to sell, he was on consignment, but he's disappeared. Alison says Ramon has gone off to college, when she realizes, he didn't, he just probably got out because he couldn't pay his debts. Lionel's boss wants to meet with them, and Lionel takes the drugs for now.
Cosima is staying at Felix's, discussing The Island of Dr. Moreau with Scott by phone; they haven't interpreted Ethan Duncan's handwritten notes in it. Felix comes in, says Cosima's been pining for Delphine, and starts setting up an account for her at an online dating service: she needs to find someone, and you can't find if you don't look.
At the Appleyard house, Gracie undresses for bed, and realizes she's bleeding. Alexis and Bonnie find her, and discover she's had a miscarriage. Bonnie tells Gracie she ruined the family's last chance, their legacy, so she's banished.
As Sarah stitches Mark's wounds, he explains his past, the Castor's all went into the military young, had no family, no outside attachments. He mentions the box of stuff that Henrik had left, and how it just had junk in it. He falls asleep (he had been drinking while being "operated" on), Sarah gets his motel room key from his jacket, and calls 911 to report his location.
Rudy is on a motorcycle nearby, and gets a phone call, leading him to the motel.
We see Helena again in her cell, now she is working on a pork bone, biting it to try to get any of it into a useful shape.
Sarah gets to the motel room, searches, and finds Henrik Johanssen's case, with just notebooks and journals in it. She finds a requisition signed by Dr. Ethan Duncan, and the form has a field that shows Henrik Johanssen was Duncan's lab assistant. She gets Cosima on the phone and explains, and sends pictures of several things in the case. Cosima scans them and notices a diary entry from Henrik reporting success in a clone-related nucleus transfer. They figure that Henrik stole the Castor samples, and made a clone with them, so they aren't looking for samples anymore, they're looking for a son of Henrik.
Alison and Donnie meet the drug supplier at night, and it turns out to be an old friend of hers from high school, Jason Kellerman. They are very happy to see each other, they had dated in high school, and had broken up, but still like each other. Alison wants this to be a business relationship, and Jason is fine with that, Alison says she knows the community and can double Ramon's business. They agree, and she's back in business.
Mark finds Sarah at the motel, and Sarah explains where Henrik's samples went; she asks if Henrik ever mentioned a son, and it turns out there was a son who didn't survive. He leads her to the house they lived in then, with a graveyard out back. He has a gun again, and says she's going to dig up the corpse.
Helena's pork bone is trimmed enough to be a useful tool; she uses it to fiddle with the lock (watching the motion of the security camera), and after several tries unlocks the cell. She goes back to the medical room with the Castor in the chair, named Parsons, and finds he is conscious, and has the top of his skull removed, with his brain exposed. He asks her to kill him. She says, "We've both been abandoned by our families, left to suffer, I make it go away." She takes a scalpel to his brain and kills him, as Dr. Coady finds her and calls for guards.
Rudy arrives at the graveyard as Sarah finds the coffin; she opens it, and there's a child's skeleton inside. She offers to give it in exchange for Helena, but Rudy isn't open to deals, he just takes the coffin. Rudy and Mark have a bit of a reconciliation, Rudy recognizing Mark as a superior, and they have the coffin, which was their goal. They look at Sarah, and remark that "we don't leave loose ends."