Emily struggles to accept the repercussions of her actions from the previous two seasons as she spends the last few days of her FBI suspension.
With the aid of his enigmatic informant Kai, Emily must work quickly to locate and save Nick.
The FBI identifies Colin Dawkins as a key suspect in Nick's kidnapping, but they are unable to locate him. In the meantime, Emily tries her hardest to keep Kai safe, and the two of them collaborate on a scheme to apprehend Dawkins and track down Nick.
Emily encounters opposition to her request that the FBI pursue Nick, which prompts her to devise a daring scheme that places her in direct contact with the only man who can guide her to Nick.
Disregarding the fact that the encryption key is not with her, Emily travels to Berlin with Dawkins to exchange the stolen files for Nick.
In Germany, Cal makes contact with Emily, and the two of them follow the lead to Jericho, where they are certain that Nick is being detained.
Unaware that Nick has attempted a daring escape, Emily makes one final attempt to exchange Kai's stolen files for Nick's life.
Nick is saved by Emily, and the two of them work out a strategy to free the refugees from the Meridian camp.
Emily gets imprisoned while she and Nick attempt to liberate the refugees from the Meridian guards. In an effort to persuade Emily to cooperate, Dawkins follows Emily's family around the farm.
The threat posed by Elliot's bioweapon remains even after Emily, Nick, and Flynn are reunited in Boston. In an attempt to keep her family safe, Emily makes a risky decision.