- Mrs. S. being forced to kill her confidants, whom she has known for years, because they had betrayed her. And her haunted look when Sarah and Kira drive off without her.
Mrs. S.: Could you just tell me why? After all we've been through together — why?
- The woman is rather sad in her final moments. She shakes and stutters, her hands impaled by knives on the table, as her old friend shoots her at point-blank range.
- Alison's grief and guilt over Aynsely's death lead her to drinking more and more. Then she learns that Donnie is her real monitor and that Felix and Sarah are skipping town, leaving her alone.
- Jennifer's video diaries. In the first one, she's bubbly and optimistic that her health will improve. But in the second one, she's horribly ill, thin and pale, her hair has fallen out, and she's been disillusioned about her chances of survival.
Jennifer: I'm going to die here.
- Felix deciding to part ways with Sarah once she starts staying with Cal.
Felix: There's no place for me here.
- Sarah tearfully telling Kira about how confused she felt growing up without any parents, making it clear that she doesn't want the same thing for her daughter.
- The ending of Governed As It Were By Chance. Sarah is knocked out by Daniel and wakes up zip-tied to a shower. He pulls out a razor and starts cutting her behind her ear...when a noise interrupts him. He leaves the bathroom and is attacked, managing only to stumble back into Sarah's view bloody and near death. Helena appears like a ghost in a Blood-Splattered Wedding Dress, prompting Sarah to scream even more than when she was being attacked. Helena slowly inches toward her sestra begging for help and gently embraces the crying, terrified Sarah.
- Helena's Wham Line: "I think he took something from inside of me..."
- Near the end of Ipsa Scientia Potestas Est Sarah tries to stop Helena from killing Rachel with a sniper rifle, telling her that she needs her help. When Helena claims Sarah just wants to use her, Sarah tearfully tells her how she felt after she had shot her.
Sarah: I thought I killed you. I couldn't tell anyone what I lost. You came back. Please put... put the gun down.
Helena: You make me cry sestra.
- Everything, absolutely everything, about Ethan Duncan. Sarah finds him a cluttered, slightly rundown old house where he lives under the Birdwatcher's protection for twenty years. One of the creators of the clones is a sweet, frail, slightly forgetful old man who made too many mistakes and now lives in fear for his life. When he first sees Sarah, he asks if she's his daughter Rachel. Then he reveals that Leekie killed his wife in the fire and was forced to fake his death; all the while his precious daughter was being raised into the cruel, cold woman who's currently trying to ruin Sarah's life. He loved Rachel so much and he completely lost the chance to watch her grow up. That's all he and wife wanted, to have a daughter and raise a family. And now all he has are his little birds.
- Sarah telling him about the the other clones, Alison and Cosima, that Cosima is sick, and practically demanding his help because she just feels so overwhelmed by the conspiracy and all that has happened to her.
- Felix drunkenly admits to Art that that he's tired of helping Sarah and hates being the guy who always gets kicked in the teeth by life because of his sister.
- Helena expressing a desire to be a mother and quietly leaving with Gracie and Mark so Hank can return the fertilized eggs to her womb.
- Rachel reunited with her thought-to-be-dead father and learns the truth about her mother's death — that the man who raised her was responsible. Despite making arrangements with Marian Bowles to eliminate him, she warns Leekie because she does still care for him. Leekie looks genuinely heartbroken when he hears all this.
- You actually feel a little sorry for Donnie when he finally learns everything that's going on and exactly the magnitude of his betrayal of Alison.
Alison: You destroyed us Donnie, with the spying and the lies. I love you so much and you ruined our family. And you're so stupid you don't even know why.
- Rachel decides to keep her relationship with her father strictly professional, even calling him by "Professor". His disappointment is palpable.
- Rachel learns that the clones are barren by design and goes on a mental frenzy. On the outside, she remains cool and controlled, but on the inside she imagines going on a rampage and destroying her office.
- At the end of Variable and Full of Perturbation, Cosima suffers a coughing fit that suddenly turns into a full-blow seizure that leaves her on the floor gasping for breath as she chokes on her own blood.
- Rachel's Villainous Breakdown is surprisingly poignant, especially when she starts to cry while starting at a picture of Sarah and Kira. If it wasn't clear before, it's clear now that she really wants to be a mother, but that option was taken away from her a long time ago.
- Sarah is very reluctant to subject Kira to an invasive procedure to save Cosima's life. Then her horror when Rachel attacks Felix and kidnaps Kira. This time, it's not a ploy by Mrs.S - Kira is really gone. No matter what Sarah does, her family is always in danger and there's nothing she can do about it short of giving up all her freedom and becoming a Dyad puppet.
- She does become a Dyad puppet in the finale, throwing away her freedom and privacy for a chance to be with her daughter. Every second of it is heartbreaking.
- Rachel admits to her father that she rewatches old tapes of her childhood because she forgot how it feels to be loved. Then Ethan commits suicide by poisoned tea to keep her from accessing his scientific knowledge of the clones because, even though he loves her, he knows she'll abuse that knowledge.
- Ethan's last words were pretty much him lamenting what happened to his daughter.
Ethan: My poor poor Rachel.