The wife of a retired cop vanishes on her way to Seattle on business. As her husband searches for her, he is asked by a friend to help with a murder case. Meanwhile, a 9-year-old girl starts behaving erratically after seeing a stranger on a beach and an assassin desperately tries to stop his secret from becoming known.

Jack searches for Amy in Seattle, but her movements produce more questions than answers. Meanwhile, Madison finds herself in a train station with a ticket to Seattle, an envelope with money, and a mysterious key. Richard suffers serious consequences due to an act of humanity.

Jack returns home and discovers a distraught and distant Amy. Meanwhile, Madison becomes determined to get to Seattle, regardless of the cost, and evade Richard's vengeance.

Madison’s instincts are gaining strength as she slowly starts to make sense of Marcus’ memories. Jack learns that Gary hasn’t been entirely truthful and forces a terrifying confession. Richard finally comes face-to-face with Marcus.

Rose confronts Jack to explain the cause of Amy’s recent strange behavior. Amy’s past – one which she has worked so hard to suppress and deny – has come back to haunt her and the only way to protect Jack may hurt him the most. Meanwhile, Richard discovers a secret about Rose that could destroy her ascent onto The Nine. Shepherd himself is skating on thin ice as Madison continues to evade his grasp.

A gruesome discovery buried in Jack’s backyard incites him to make one last attempt to bring Amy home. Rose remains haunted by a tragedy from her distant past and abducts a lowly waiter whom she’s certain will have answers. Tired from running, Richard confesses to Rose the truth about Marcus’ return, while Marcus gets ever closer in exacting his revenge against Rose. Gary has finally realized how to expose the corruption behind Qui Reverti, but it demands an unthinkable sacrifice.

In the season finale, Jack discovers the alarming depth and scope of the organization to which he’s lost Amy. Marcus and Madison engage in a fatal struggle. Richard is forced on the run but recruits an unexpected partner along the way.