Season 2

Complete listed story — includes the ending

1. Nature Under Constraint and Vexed

Sarah runs to a nearby diner, where she is quickly confronted by two armed men, one of whom is Mark Rollins, who attempt to bring her in. They kill the diner's owner (who shoots one of the men in the process), but Sarah manages to escape. She finds Felix and gets Alison to give them access to an unregistered gun so she can get Rachel to bring her to Kira and Mrs. S, as she believes Dyad has kidnapped them. Sarah impersonates Cosima at Dyad to steal Leekie's passkey and confronts Rachel, who reveals she does not have Kira. Alison, who tries to kick her addiction to pills, is chosen as the lead in the community musical, replacing the now-dead Aynsley. Leekie wants Cosima to start working for Dyad. With nowhere else to go for help, Sarah goes to Art's home with the intention of telling him the whole story. Art, who is investigating the diner shooting, identifies the perpetrators as Proletheans; they are likely the ones who have Kira. Meanwhile, a wounded Helena stumbles into a hospital.

2. Governed by Sound Reason and True Religion

Kira calls Sarah, and Art traces it to a motel. Sarah gets kidnapped, while Art has a run-in with Daniel that later results in his suspension. Sarah is taken to Mrs. S, who reveals she ran away with Kira and made it look like a kidnapping. They go to a country house owned by two compatriots. Later that night, Kira admits she no longer trusts Mrs. S, so she and Sarah attempt to escape. Mrs. S learns that her compatriots plan to sell Kira to the Proletheans; she kills the two to allow Kira and Sarah to escape. Meanwhile, during Aynsley's funeral, Alison begins to suspect that Donnie was her monitor all along, so she and Felix set a trap for him that confirms her suspicions. Alison returns to drinking from the guilt of Aynsley's death. Cosima and Delphine set up a new lab at the Dyad institute to learn more about the former's condition. Art's partner Angela Deangelis learns of Helena's existence, but when she visits the hospital, Mark has taken Helena away to a ranch owned by Henrik Johanssen, the Prolethean leader who plans to use Helena to create a baby. Henrik has Tomas killed for objecting to his plan.

3. Mingling Its Own Nature with It

Sarah, Felix, and Kira arrive at a house belonging to Cal Morrison, who is revealed to be one of Sarah's marks and Kira's father. He allows the three to stay for a little while. Felix returns to the city to support Alison in her play. Angela tries, and fails, to befriend Alison to learn more about the lookalikes. Before the play's debut, Alison drinks too much, then falls off the stage during her performance. Cosima and Delphine investigate the death of Jennifer Fitzsimmons, a clone who died from the same respiratory illness as Katja and Cosima. They autopsy the body and believe that the illness is possibly linked to the clones' infertility. Art begins to surveil Henrik's ranch, as Henrik marries Helena, then takes her away to a room. Daniel, who spent the episode looking for Sarah, tracks her down and kidnaps her, while also murdering a local police officer. Cal finds them, and he crashes his truck into their car.

4. Governed as It Were by Chance

Cal and Sarah hide the car and the assumed-dead Daniel. Sarah leaves Kira with Cal and returns to Mrs. S's home with Felix, where they find news clippings of Susan and Ethan Duncan, the founders of Leda and the cloning project and Rachel's adoptive parents. Mrs. S, meanwhile, reunites with Carlton Redding, who helped smuggle her and Sarah out of London. Helena escapes from the ranch after Henrik's daughter Gracie tries to kill her and remembers that Henrik took something from her. Alison wakes up in rehab. She is told by Donnie that she will not see her children unless she stays a week. Sarah sneaks into Rachel's apartment, only to be captured by the very much alive Daniel. As he tortures her, Helena arrives and kills Daniel. At the ranch it is revealed that Henrik took Helena's egg cells for in vitro fertilization.

5. Ipsa Scientia Potestas Est

Rachel has Paul replace Daniel as her monitor and lover, while also withholding a stem cell treatment from Cosima. Despite this, Leekie plans to treat Cosima anyway. He later confides in Cosima that the original clone genome was lost in a lab fire; the genome would have provided the cure for the illness. Meanwhile, Paul, under Rachel's orders, storms in on Felix and gets his fingerprints on Daniel's gun to frame him for the police officer's murder. He gives Sarah until morning to produce Kira. Sarah places Helena in Art's custody so she can learn more about the Proletheans. Helena escapes, but provides Art and Sarah with clues to the location of Maggie Chen's locker. There, the two find clues relating to Ethan Duncan's location and realize that Helena intends to assassinate Rachel. Sarah finds Helena and talks her out of killing Rachel, and under Leekie's promise that he will drop the charges against Felix, the two set off to find Ethan.

6. To Hound Nature in Her Wanderings

Sarah and Helena arrive at a church where Ethan has been. Sarah visits the archives to learn more about Ethan, and with the aid of Art and Felix investigating the files from Maggie's locker, learns that he changed his name to Andrew Peckham. Helena finds a bar and makes a connection with local man Jesse, but she is later arrested for fighting with some drunks. Mark and Gracie later invite Helena back to Henrik's ranch to allow herself to be inseminated with her own fertilized eggs. Scott Smith, a fellow student of Cosima's, joins her and Delphine at Dyad, and learns that the stem cells Cosima was given belong to Kira. At rehab, Alison befriends Vic, who is later revealed to be an informant for Angela to get dirt on Alison. Sarah arrives at a house only to find Mrs. S, whose old contacts have protected Ethan for years. Sarah meets Ethan, who informs Sarah that he started the clone project before it was hijacked by Leekie and the neolutionists in 1977. He also fears Leekie, who was behind Susan's death.

7. Knowledge of Causes, and Secret Motion of Things

Alison reveals to Vic that she let Aynsley die, then learns he is Angela's informant. Vic promises not to tell Angela if he sees Sarah. Sarah sees Vic at rehab, but Felix has drugged him, and he collapses. As Alison and Felix hide Vic, Sarah is mistaken for Alison and is forced to attend "Family Day," ultimately resulting in Donnie finding out about the clones and that Alison was telling the truth about being probed. Mrs. S and Paul arrange a meeting between Rachel and Ethan. After Ethan tells Rachel of her mother's fate, Rachel fires Leekie, and also implies to him that Dyad will be after him. Cosima is angry with Delphine for using stem cells from a tooth Kira lost during the car accident. Kira willingly decides to give Cosima another tooth for analysis. Donnie goes to confront Leekie for lying to him and accidentally shoots him in the head.

8. Variable and Full of Perturbation

Art receives a call on Beth's old cell phone from Tony, a transgender clone who promised his dying friend, Sammy, that he would deliver a message to Beth. Tony stays at Felix's apartment until Sarah arrives to tell him that Beth is dead and reveals his origin. Tony delivers the message: "Tell Beth to keep the faith. Paul's like me. He's on it. He's a ghost." Alison learns Donnie intends to leave, prompting her to admit to being responsible for Aynsley's death. Donnie confesses to killing Leekie, and the two begin work to cover up the murder. Sarah and Mrs. S agree to transport Ethan Duncan to Dyad to start work on a synthetic therapy that may cure Cosima of her illness. Ethan reveals to Rachel that the clones were always intended to be infertile, and views Sarah as a "failure." Before leaving, he hands Kira the book The Island of Doctor Moreau, which houses all of his secrets in its margins. As Ethan and Cosima begin to work, Cosima collapses and goes into violent convulsions.

9. Things Which Have Never Yet Been Done

Rachel appoints Delphine as Leekie's replacement for director of clone research. Learning that Kira's bone marrow might save Cosima, Sarah asks Kira to donate some, and Kira agrees. As Alison and Donnie work to bury Leekie in their garage, Vic returns to either blackmail her or discover new dirt for Angela. Suspecting that Angela's operation is not official, a newly assertive Donnie confronts Angela to chase them both away. Burying Leekie causes the couple to have a newfound passion, and they have sex. Helena and Gracie are implanted with Helena's eggs fertilized with Henrik's sperm. Helena finds out that Henrik intends to impregnate several other women with Helena's eggs. Helena helps Gracie and Mark run away while she kills Henrik and burns the farm down. Rachel, disillusioned at the prospect of not being able to have children, tricks Delphine into distracting Sarah while Rachel, posing as Sarah, abducts Kira.

10. By Means Which Have Never Yet Been Tried

Sarah surrenders to Dyad hoping to secure Kira's safety but is imprisoned. Rachel deliberately separates Delphine from Cosima by sending her to Germany. Ethan commits suicide to prevent Rachel from getting the code key. Kira steals a cell phone and contacts Cal, who goes to Mrs. S. They meet Paul, who is revealed to be in the military, and Marion Bowles, a Dyad executive. Scott and Cosima devise a plan to break Sarah free by making a makeshift weapon out of a fire extinguisher. Rachel sabotages Cosima's treatment by destroying the bone marrow, at which point Sarah uses the weapon, shooting a pencil into Rachel's eye. They all escape Dyad with the aid of Marion, who invites Sarah to meet her the next day. The next morning, Helena leaves, but is kidnapped by the military as arranged by Paul and Mrs. S. Kira gives Cosima Ethan's book with the sequences needed to save her life. Sarah visits Marion's home, and meets Charlotte, a clone of Kira's age and the only survivor of the second Leda batch. Marion explains that the military controlled a male clone project, Castor, with the clones looking like Mark.