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At the Institute, Sarah passes a likewise-handcuffed Ethan Duncan in the halls. The professor instructs her not to despair and then is shuffled down the hall while Sarah is led into an elevator. In a video room playing home movies of young Rachel's life with her father, Ethan is confronted by Rachel yet again. In a showdown of the minds, they drink tea and war back and forth with each other. Rachel demands that Ethan "unlock" another clone and in exchange the Dyad would save Cosima. Ethan flips the demands, stating that he won't even consider another clone until Cosima is cured. Rachel yet again demands the key to Ethan's cipher, which prevents the creation of more clones, and Ethan bluffs that he never wrote the cipher down but instead only kept it in his mind. Once they come to an impasse, Ethan asks Rachel if she remembers how much he and her mother loved her and Rachel admits that she has no memory of their love at all. Ethan appears overly emotional at the admission but in reality is reacting to the poison he laced his own teabag with. In his last moments, Ethan tells Rachel he doesn't believe she deserves him any longer.
Cosima has been granted time with Kira and the pair engage in a small science experiment of their own. Cosima teaches Kira about force by having her try to push a pencil through a piece of construction paper. As the science experiment ensues, scenes of Cosima and Scott preparing their own experiment mix in. We're not given a clear idea of what they're making, but it's implied that is has to do with force, much like Kira's experiment, only on a much larger scale. Unfortunately, Cosima's illness has gotten the better of her and she can't complete the experiment. However, the ever-impressive Scott produces a Dyad keycard and convinces her to let him follow through as it's their only chance for success.
Sarah is stolen from her room and pulled into a terrifying, impromptu surgery. As she's secured, Scott appears in guise of a surgeon and loosens her straps just before Dr. Nealon approaches. He tells Sarah that they are performing an oophorectomy, or removing one of Sarah's ovaries, for research purposes. And as if Dr. Nealon wasn't bad enough, in walks Rachel. She sends everyone out of the room and shows Sarah Kira's bone marrow, now in her possession, and a picture from Kira depicting the mother/daughter pair and a large fire extinguisher.
Rachel proceeds to tell Sarah that Ethan is dead, though Rachel believes that Sarah is actually in possession of Ethan's cipher. When Sarah is unaware of the cipher's location, Rachel smashes Kira's bone marrow on the floor and begins to leave the room. Sarah calls her back and quickly reaches for the handle of the fire extinguisher next to her, which projectiles a sharp pencil straight into Rachel's left eye. Scott swoops in and hands Sarah a Dyad keycard so she can to save Kira and escape.
Sarah hurries to Kira's room just in time to see Marian Bowles preparing Kira to leave the Institute. She tells Sarah that they are free to go of their own accord and that she'll give Sarah all the information she wants if she agrees to meet Marian the next day. Felix brings Helena to his loft and the Ukranian clone is brought face to face with her entire sestra family, for the first time in two seasons. The feels just keep on coming as Helena is embraced by Cosima, Alison, and lastly Kira, all of whom are happy to see their long-lost relative. The most touching scene of the season includes a dance party between all clones to a great reggae soundtrack.
The morning after the clone sleepover, Cosima and Sarah have a moment alone to discuss Cosima's impending death. Meanwhile, Helena wakes and after leaving the case housing her embryos at Felix's apartment, decides to step out. Her motive isn't exactly detailed, but there's not much time to ruminate on that as her head is immediately covered with a black bag and she's incapacitated by an electrical Taser, then carried off by two nameless men.
Kira comes to Cosima's bedside to wake her but doesn't get a response. It takes several shakes for Cosima to rouse and this happens only after Kira touches the clone's face. With storytime in mind, Kira hands Cosima the copy of The Island of Doctor Moreau gifted to her by Ethan Duncan, which allows Cosima sees all the sequences outlined in the book's margins.
Meanwhile, Sarah meets with Marian Bowles at her lavish house and comes face to face with a little girl who looks remarkably like young Rachel from her home videos. Marian explains that Charlotte is definitely a clone, the only one of 400 failed Dyad experiments, and that Marian is Charlotte's adoptive mother. The information just keeps on flowing as Marian explains her role in the Dyad. Her company, Topside, helps steer the Dyad Institute along with other large, multinational corporations. Their primary role is to secure money to help the Dyad's research in technologies to help the future, including synthetic biology and genetic engineering.