Sydney must decide whether her mother's goodwill gesture was sincere or an attempt to kill her. Will witnesses Francie discussing her restaurant plans with a man whose affiliations are questionable, and Sloane is made a full partner in the malevolent Alliance of Twelve.

Sydney must outwit Sark in order to find a crucial piece of intel. Meanwhile, Jack faces Sydney's mother for the first time in almost 20 years. Will finally meets Vaughn and Sloane is haunted by his wife's death.

Sydney's trust in her father begins to fade. Meanwhile, Sydney and Vaughn may have been exposed to a deadly virus while in Taipei; Sloane haunted by Emily's death begins to unravel. Vaughn enlists Will to help research a case.

Sydney and Jack are confronted by the new director of SD-6 who replaces Sloane, whose whereabouts and intentions are unknown. Meanwhile, romantic sparks begin to fly between Francie and Will.