Rachel has kidnapped Kira and Mrs. S. While trying to elude Rachel's thugs herself, Sarah has to decide whether to trust Paul as the person who has the best access to Rachel of those she knows in order to get Kira back. All Paul does tell Sarah is that there is a black tie event at Dyad at which Rachel will be in attendance. Sarah decides that she needs to attend the event - Cosima who already is an invitee - but has no plan beyond knowing that she will need to get in there with concealed gun in hand. With this scant outline of a plan, Sarah enlists the help of Felix and the other clones, although Sarah does end up enlisting their help also without their knowledge. Meanwhile, Cosima has decided to trust Delphine, Cosima's grand plan which is to take control of her own "biology" in dealing with her illness, as opposed to providing Leakie with this information. Alison wants her life to return as close to suburban normal as possible, which includes immersing herself into her community theater production, a possibly difficult task as the spirit of Aynsley hangs over the production. And Art and Angela are no longer officially working on the case as there is no case to work on, but they cannot let go of what little information they have on hand, especially as Art knows that Sarah was about to tell him everything just before she was sprung from jail.

On information from Art, Sarah learns that it is not Rachel who abducted Kira, but rather the Prolethians, the reasons she does not know behind the abduction. However, there is no news whatsoever about Mrs. S, who she believes must have also been abducted along with Kira, which is only of little concern to her based on what her birth mother told her before her death. Regardless, Sarah decides to trust Art so that he can help her locate Kira. What Sarah discovers in the matter is not quite what she expects, which results in her not knowing who to trust. Art also tries to convince Angela to leave matters alone as he is not prepared to tell her everything that Sarah has told him. The Prolethians are also able to recapture Helena. Cosima tries to convince Leakie that she is not working with Sarah - that Sarah is indeed the enemy - and thus had nothing to do with Sarah infiltrating the event at Dyad using her identity. Cosima runs into a roadblock in taking over the research into her own biology, but is provided another task concerning the biology of the clones as a collective, but which focuses on Sarah. Felix is able to convince Alison that it is Donnie who is her monitor and not Aynsley. This news places Alison in a bad state as she deals with her involvement in Aynsley's death, but she and Felix also know that they need to catch Donnie in the act as conclusive proof.

Sarah is able to escape with Kira from the bird watchers and Mrs. S, and now, along with Felix, are on the run with no money. They decide to take refuge at a secluded house where the owner seems to be away. But the choice of the house is no accident. This stop has an unintended effect on Felix. As Alison prepares for opening night, she slowly begins to unravel under all the pressure, which includes meeting someone who she believes is another monitor. Cosima learns from Delphine of yet another clone, Jennifer, who recently died from whatever ails Cosima herself. They hope that her death can help them figure out what's wrong with Cosima before it's too late for her. Gracie begins to doubt the plan that her father has for Helena "joining the family". And Art finds out that Angela has been snooping around despite him telling her to leave things alone.

Sarah survives the car crash, is quickly reunited with Kira and sets off with Cal in his camper. She decides to head back to the city to find out from Mrs. S just what is going on. She also pays a visit to Rachel which doesn't quite go as expected. At the Dyad Institute, Cosima takes on the task of finding out about Project Leda. Alison awakens from her drug and alcohol stupor to find her right arm in a sling - and that she's in a rehab clinic. Felix convinces her she should spend a week there and just rest. Henrik Johanssen makes it clear to his daughter Gracie that Helena is part of their family. Gracie isn't so accepting. Art is still snooping around with his camera and sees Helena.

Rachel returns home to find Rosen dead, which she takes out on Sarah and Cosima. She also makes Paul an offer he can't refuse, even if he wanted to. In this new position, Paul decides to use Felix to help Rachel. Leekie, unlike Rachel, shows that his plans veer toward the truly scientific, he who provides Cosima and Delphine with some information about the clones' past. Feeling indebted to Helena for saving her from Rosen, Sarah decides to help Helena within the bounds of what Sarah believes is right. Helena may have thoughts of her own about what she wants to achieve. But she also provides both Art and Sarah with some information about Maggie Chen, which they in turn use to find out more about Rachel's past. Cal and Kira are still hiding out in Cal's motor-home, Kira who hints about Sarah's "sisters". And Henrik and Bonnie have Gracie confined for what she did regarding Helena, which Gracie may have to pay for in more ways than one if Helena is not retrieved.

Sarah and Helena are traveling together to Cold River to find out more about their clone past and specifically the person who Helena refers to as the Swan Man. This trip marks the first time that Helena has felt a sense of freedom in a long time. This freedom, however, may ultimately cause problems for her. Sarah's quest for information takes her to some unlikely places, or more precisely to some unexpected people. She gets some help in this quest by Art and Felix, who have the information obtained from Maggie Chen's storage unit. Felix, however, is often in a state where he isn't much help. But what Sarah discovers may be all for naught if the people who are tracking her and Helena independently, namely Paul and Mark, are able to accomplish their mission in abducting the pair. Cosima is as worried about her own health as she is about Sarah's concern over getting Cosima's affliction. But Cosima has other more pressing concerns in the form of the new addition to the research team, that person who seems to know more about what's going on than she would like. Alison runs into a familiar face in rehab, that person who she is slow to warm to. However, he also being in rehab may not be all a coincidence.

When a rehab confidante betrays Alison and threatens to expose the truth about Aynsley's death, she goes into free fall on the eve of Family Day. With Donnie and the kids set to visit, it's all clones on deck to contain the fallout.

A new player in the clone conspiracy turns up at Felix's door, sending him into crisis mode. With Cosima running out of options, Sarah struggles with the decision to surrender a crucial piece of leverage and make a deal with DYAD.

Cosima takes a turn for the worse, forcing Sarah to take desperate action - with tragic consequences for those she loves. The Proletheans set their ultimate plan in motion. Alison and Donnie tangle with the law.

After the successful abduction of Kira, Sarah prepares to surrender to Rachel and the Dyad Group; but the Clone Club has other ideas as they band together to pull off the ultimate rescue.