Emily tries to get her memory back after she leaves the hospital, but Howard grows impatient with her as he tries to avoid detection at home. Meanwhile, Quayle tries to bolster his position against Temple.
Howard's loyalties are tested when he is imprisoned on the other side, while Emily Prime is offered a promotion and to have Howard freed if she helps with a case.
Howard is transferred to a new prison. Meanwhile, as Emily receives a mysterious visit, her past comes surfacing.
With a common enemy back in the scene, Howard Prime, Quayle, and Clare must join forces to combat him. Emily Prime investigates her other, while Yanek makes discoveries about Howard's past.
Howard Prime and Quayle are in danger when a new revelation is made. New events disrupt life at Echo Prison, while Clare gets in touch with her past.
A flashback reveals the truth about how Yanek contributed to the creation of duplicate parallel worlds and the consequent crossings. In the present, Mira issues an ultimatum demanding to close the Crossing.
Suspicions rise around OI in the aftermath of the lockdown. Meanwhile, Emily and Howard Prime run into new evidence about the Management, while Clare questions her allegiances.
Emily and Howard Prime try to figure out what Indigo's plans are, while Clare and Quayle think about the future. Howard must contend with a new revelation about his wife.
A new decision is made by the Management, as Emily sends another ultimatum. Quayle, Temple, and Clare examine the last Indigo cell, while Howard Prime seeks help from an old acquaintance.
Things escalate when the overlap between the two worlds turns into chaos. Howard decides to use Quayle's wife for a serious bargain. Howard discovers that cowardice is the only thing that has kept him from deciphering what happened to his wife. Mira gets new alliances.