Which brings us to the most important part of Orphan Black: what the hell is going on?
It doesn't seem like anyone knows. Towards the end of the season, Sarah has no idea what's happening; Cosima is still trying to balance her research of the cloning experiment with her budding love for Delphine and her simultaneous distrust of her; and Alison is having what appears to be a complete mental breakdown because, you know, her whole life is a sham and she was created in a laboratory by a bunch of scientists. Can you blame her?
As previously specified, Helena kidnaps Sarah's daughter Kira, but, after about five minutes, lets her go when she realizes she doesn't want to hurt her, or Sarah. Kira sees Sarah frantically looking for her in the distance and runs toward her, only to get hit in the middle of the street by a car. Sarah rushes her to the hospital, understandably frantic, and luckily finds out that Kira is going to be OK.
Meanwhile, Mrs. S has been searching for Sarah's birth mother, Amelia, and ends up finding her and bringing her to Toronto. While this is good news in the beginning (Sarah is thrilled to meet her), its not that great when Sarah takes Helena to meet her in an effort to show Helena that the Proletheans have been lying to her all her life. Their mother explains that the pregnancy was a surrogate one and that when she discovered that the Dyad Institute was shady as fuck, she gave them both their best chance of survival by splitting them up, and going into hiding herself. Helena doesn't believe it at all.
Not much later, she poses as Sarah and visits Amelia at Beth's old apartment where she's staying. Just as Amelia is telling her to watch out for Mrs. S, Helena begins to speak with a Ukrainian accent and then guts her with a knife. Zoinks!
When Sarah finds Helena with Amelia, nearly dead, Sarah understandably loses her shit and gets into a major fight with Helena. Sarah eventually shoots Helena as she tearfully says, "You killed someone I've been dreaming about my whole life." Helena is presumed dead.
Also worth noting: before Amelia dies, she gives Sarah—the real Sarah—a picture dated 1977, featuring Mrs. S herself as a scientist working for the Dyad Institute. That's suspicious!