On November 23, 2012, small time con artist Sarah Manning (Tatiana Maslany) sees Elizabeth Childs, a woman who looks just like her, commit suicide by jumping in front of a train. With the help of her foster brother Felix Dawkins (Jordan Gavaris), Sarah fakes her death while assuming Beth's identity to clear the $75,000 from her bank account in order to get her daughter Kira back, as well as to escape from her abusive ex-boyfriend Victor Schmidt (Michael Mando). Sarah soon learns that Beth was a police detective who is currently suspended following the shooting death of civilian Maggie Chen. Furthermore, Beth was secretly investigating several women from across the world with similar birthdays to Beth and Sarah (late-March to early-April 1984). Beth's partner Arthur Bell (Kevin Hanchard) begins following her after becoming suspicious of his "colleague". While Sarah oversees her funeral from a distance, she is approached by Katja Obinger, another lookalike who later discovers Sarah is not Beth. Katja is then killed by an assassin, and Sarah narrowly avoids the same fate.

Sarah must pose as Katja to find a mysterious suitcase. As Sarah delves further into the mystery of her lookalikes, she meets Alison - another lookalike who may provide her with the answers she needs.

Sarah meets Cosima, another lookalike. Cosima and Alison reveal to Sarah all that they know about what is happening with the lookalikes including that they are clones. As Beth, Sarah must investigate the death of the body she buried.

Alison impersonates Sarah to help her with Kira while Sarah encounters the person responsible for the deaths of other clones.

The women learn that they have monitors - people in their lives whose purpose it is to observe them. They then try to discover who the monitors are.

Alison ties up and interrogates her husband after suspecting him of being her monitor - but is he her monitor or just her husband?

The Neolutionists discover Sarah is not Beth-as Helena reappears to Sarah. Delphine pushes Cosima towards Dr. Leekie. The police department moves closer to the truth.

Paul tries to cover up Sarah's existence. Alison takes vengeance on her suspected monitor, which could cost her everything she holds dear.

Sarah rescues Helena from Tomas and must decide what to do with her. Cosima faces the truth about Delphine and Sarah comes face to face with her birth mother for the first time.

Alison, Cosima and Sarah must decide whether to trust their creators. Cosima works to uncover more about herself and the others - with Delphine's assistance. Sarah discovers more about her birth, her connection to Helena and is forced to make a decision about Helena.

Sarah seeks the comfort of Felix and confronts Rachel in an attempt to convince her to release Mrs. S and Kira, while Cosima and Delphine further examine Cosima's biology and respiratory illness. Alison takes up acting to help her recover from the loss of Aynsley and enlists the services of Ramon, an unregistered weapons dealer, to help further Sarah's cause.

Sarah, Mrs. S, and Kira seek shelter at a safe house full of secrets, while Art attempts to keep Angela from discovering the truth. Cosima struggles to assimilate to her new surroundings at the Dyad Institute. Alison spirals emotionally as she attempts to cope with her killing of Aynsley and her realization that Donnie is her monitor. Helena is rescued by the Proletheans.

Sarah and Kira seek asylum at the home of Cal Morrison, one of Sarah's past lovers. Felix returns to the city to support Alison in her play, as her mental health suffers a downward spiral. Cosima and Delphine investigate the death of Jennifer Fitzsimmons, a clone who suffered from the same respiratory illness as Katja and Cosima. Daniel furthers his search for Sarah and Kira, while Art delves deeper into the mystery surrounding the Proletheans.

Sarah, Cosima, and Felix dig further into Mrs. S's past, leading them unexpectedly to Rachel's origins. Alison admits herself into rehab for her alcoholism but is forced to stay when Donnie intervenes. Helena escapes from the clutches of the Proletheans while Art scouts the perimeter of the compound. Cal protects Kira from harm as Sarah attempts to further uncover the mysteries in Rachel's past. Mrs. S rekindles an old flame.

Rachel wages war against Sarah, threatening the lives of everyone close to her. Sarah and Art continue to search for answers regarding Rachel's past while Helena goes on the offensive against Rachel. Cal continues his guardianship over Kira, and the Proletheans resort to extreme measures in order to further their goals. Leekie agrees to administer a new treatment for Cosima's illness against Rachel's orders as Paul succumbs to Rachel's influence.

Sarah and Helena embark on a road trip to Cold River to find Ethan Duncan. Helena's journey is interrupted by the appearance of Mark and Gracie, who try to convince her to return to the Prolethean compound. Art and Felix review the contents of Maggie Chen's locker to help Sarah in her quest. Sarah finds the home of Ethan Duncan, confronts an unexpected visitor, and learns important secrets about the clones' origins. Scott joins Cosima and Delphine at the Dyad Institute, discovering key genetic anomalies; while Alison encounters a familiar face at rehab.

Cal is forced to move Kira to a new location after his cover is compromised. Sarah leaves Ethan Duncan in the hands of Mrs. S in order to reconnect with Kira. While Alison and Vic prepare for Family Day at the rehabilitation center, Alison discovers Vic's plan to reveal her darkest secrets to Deangelis. Cosima begins the treatment for her respiratory illness while Delphine comforts her. Rachel reconnects with her father, as Leekie consults with Rachel's superior, Marion Bowles, about Sarah Manning. Alison reconnects with her children and confronts Donnie about his role as her monitor. Cosima discovers the truth about the origin of the stem cells used for her treatment, and Sarah regains guardianship over Kira. Donnie confronts Dr. Leekie.

Art receives a call on Beth's old cell phone from Tony, a transgender clone who promises his dying friend, Sammy, that he will deliver a message to Beth. Sarah and Mrs. S agree to transport Ethan Duncan to the Dyad Institute, hoping that his synthetic therapy will cure Cosima of her illness. Before he leaves, Ethan gives Kira a children's book that houses all of his secrets in its margins. Rachel takes control of the Dyad after Leekie's demise, and Cosima reveals 324B21's true identity to Scott. Felix houses Tony at his apartment and calls Sarah for help. Sarah arrives and reveals the truth behind Tony's origins, and Tony reveals Sammy's message, which implies that Paul may have a secret agenda. Alison helps Donnie cope with his killing of Dr. Leekie, and the two take measures to cover up the event. Cosima collapses and convulses in the presence of Delphine, Ethan, and Scott.

Kira undergoes bone marrow extraction in the hopes of halting the progression of Cosima's sickness. Ethan, Scott, and Cosima work to unlock the genetic sequences that caused the clones' respiratory illness. Rachel promotes Delphine to the position of Dyad director and begins to unravel emotionally, causing her to resort to drastic measures in order to further her goals. Alison and Donnie confront Vic and Deangelis while attempting to dispose of Leekie's body. Helena seeks vengeance against the Proletheans and helps Gracie and Mark escape from Hank's oppressive clutches.

Sarah surrenders herself to Dyad in an attempt to secure Kira's safety. Rachel transfers Delphine to Frankfurt so that she is no longer able to associate with the clones. Ethan makes the ultimate sacrifice in order to ensure that Project Leda does not continue. Kira steals a cell phone from a nurse and calls Cal who later appears at Mrs. S's door with key information that he learned after hacking into the computer of a Dyad double agent. Cal and Mrs. S make contact with the informant and ask for help releasing Sarah. Cosima, Scott, and Kira devise a plot to help Sarah escape. Mrs. S, Cal, and Paul, who is now a major in the military, confront Marion, the high ranking Dyad official who outranks Rachel and Dr. Leekie, who agrees to release Sarah but stipulates that her safety once released relies solely on herself. Sarah is taken into an examination room to undergo an oophorectomy, and is able to escape Rachel's clutches with Scott's assistance. Scott gives Sarah an access card, and she enters Kira's to find Marion already preparing Kira for departure. Marion tells Sarah to visit her home if she wishes to find out answers to her questions. Sarah, Helena, Alison, and Cosima congregate in Felix's apartment. Helena leaves in the middle of the night and is kidnapped by two men. Sarah visits Marion's home the next day and encounters Charlotte, the last living clone of the 400 attempts that were made to perpetuate Project Leda. Kira shares with Cosima the special book that she was given by Ethan before he was taken to the Dyad Institute. Helena is escorted by the military to a plane as Mrs. S and Paul watch from a distance. Marion reveals key information about the clone experiment.