Mysteries unfold as Amy heads to Seattle on business and vanishes; Jack goes to Seattle only to uncover more unanswered questions about Amy's whereabouts; an old friend visits Jack and asks for his help. Meanwhile, nine-year-old Madison starts behaving erratically after seeing a stranger on the beach. An assassin desperately tries to stop his secret from leaking.
Jack desperately tries to find Amy in Seattle but her movements offer more questions than answers; Madison finds herself in a train station with a ticket to Seattle, an envelope of cash, and a mysterious key. An act of humanity has serious consequences for Richard.
Jack returns home to find Amy sleeping soundly in bed. She has a logical explanation for her whereabouts in Seattle and professes her love to Jack only to ask for a separation the next day. Jack is terrified for Amy's mental state. Meanwhile, Gary calls with alarming news. Things get dangerous as Madison hitches a ride to Seattle, determined to evade capture. A deal from Richard's past continues to haunt him.
Gary reveals a strange link between his former client and Amy. But just as Jack and Gary start to put the pieces together, their only reliable source is brutally murdered. Meanwhile, Madison arrives in Seattle and threatens an old acquaintance. Richard attempts to conceal his secret continues while handling rising pressure from Rose.
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 - 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. 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.