Having woken up in Hong Kong, with no memory for the last two years (!), Sydney returns to Los Angeles to try to piece together the last two years of her life and discovers the fates of her friends and family: Vaughn has married thinking that Sydney was long dead; Marshall is having a baby with CIA tech expert Carrie Bowman; and Dixon is now the new division head of the L.A. office branch of the CIA. Sydney also learns the shocking fates of Jack and Sloane; the former is in CIA custody for communicating with Irina whom still is in hiding, while the latter is living in Switzerland under house arrest in exchange for co-operation with the CIA. Sydney is granted temporary CIA clearance on a case that may help her regain her memory and she meets a new enemy group called The Covenant.

Sydney's emotions are turned inside-out when she once again comes face-to-face with Allison Doren, the murdered Francie's doppelgänger, who was presumed dead but is now a key assassin working for the Covenant. Meanwhile Lauren's search for Lazarey's murderer leads her closer to discovering the connection to Sydney, and Sydney begrudgingly is assigned as Sloane's CIA handler.

Jack contacts a mysterious woman, that of former KGB agent Katya Derevko, Irina's older sister, to help him free Sydney and Vaughn, whose plane has crashed inside North Korea while seeking to find a defecting Russian scientist, named Leonid Lisenker, whom Sark is trying to kill before turning himself to the CIA. But Jack is faced with a curious conundrum when Katya tells him that she will not put the rescue plan in motion until he fulfills a favor: assassinate Sloane.