Season 2 begins with Sarah searching for her missing daughter and suspecting that ruthless pro-clone Rachel is behind the disappearance. Meanwhile, Alison attends the funeral of her fallen friend, Aynsley, which causes Alison to sink into despair.
Sarah gets Art to help her find Kira and is shocked when she learns where the trail leads. Meanwhile, Alison struggles with Aynsley's death; and Cosima grapples with the worsening symptoms of her mysterious sickness.
Sarah turns to an old flame from her past as she hits the road with Felix, but their brief respite is brutally shattered. Sarah then realizes that no matter how far she runs it will never be far enough.
Sarah joins forces with an unlikely ally, when she follows a trail of clues that she hopes will lead her to the origins of the clone experiment. Meanwhile, Cosima and Delphine make a discovery that could prove to be the key to treating Cosima's illness.
A rehab confidante betrays Alison and threatens to expose the truth about Aynsley's death, which causes Alison to go into a free fall on the eve of Family Day. The clones gather to contain the fallout.
A new player in the clone conspiracy emerges and turns up at Felix's door, which sends him into crisis mode. Meanwhile, Sarah struggles with whether to surrender a crucial piece of leverage and strike a deal with Dyad.
Cosima takes a turn for the worse, which forces Sarah to take desperate measures that result in tragic consequences for those she loves. Meanwhile, the Proletheans set their ultimate plan in motion; and Alison and Donnie tangle with the law.
Season 2 ends with Sarah being forced to concede when Rachel launches her latest ploy. However, the Clone Club springs into action to save her. Later, Sarah meets a new ally and uncovers a terrifying new dimension to the conspiracy.