Nadia is kidnapped and her life threatened by Sydney's old enemy Anna Espinosa. Vaughn is forced to make a deal with Sark in order to save Nadia, despite the inner demons he is forced to confront upon seeing is old enemy.
Sark agrees to help the FBI, but only if he and Vaughn open Lauren's casket so Sark can see for sure that Lauren is dead. Jack revives Nadia from a coma to get information, but the result could mean Nadia's death.
During a staged mission and CIA hearing, Sydney "quits" the organization to cover the fact that she, Jack, Vaughn, and Dixon have been recruited into a special covert branch of the CIA.
Sydney and Jack argue about Sydney's telling Nadia the truth about Irina's death. Sydney goes undercover to get close to an arms dealer so that she can discover the location of a missing code-breaker. Vaughn thinks that Weiss may have died on a mission.
Sydney and Vaughn are sent undercover to find a bio-weapon, with her pretending to be a social worker and he a drunk priest. But Sydney soon grows concerned that Vaughn is still distraught over having to kill Lauren. Nadia wants information regarding her mother and turns to Jack for the answers.
Sydney and Vaughn pose as a married couple in suburbia to find a weapon that could send society back to the Dark Ages. But in the process of their cover, they find their own relationship strained.
Sydney is infected with a deadly hallucinogen. Jack and Vaughn try to discover who created the drug and find an antidote before Sydney turns violent and possibly suicidal.
Sloane shows concern for Nadia's well-being while she is on a mission with Sydney to find the whereabouts of deadly chemicals. But Sydney and Nadia argue about whether Nadia should truly believe in Sloane's fatherly affection.
Sloane initiates an operation to steal a decoder from French police that causes Dixon and Sydney to think that Sloane is trying to re-form the Alliance. Their plans threaten to ruin Sydney's relationship to Nadia.
Jack hunts down and murders an old associate who learned all of his skills from Jack. Sydney steals the pass card of a busboy at a night club run by a terrorist and then has to protect the busboy and herself from his employer. Vaughn looks into the possibility his father is alive.
Nadia is tortured by memories of her life after leaving the orphanage and fails to confide knowledge of a previous relationship with an enemy in her current mission. Vaughn discovers more information with Sydney's help about his father's past and meets up with a woman also from Nadia's past.
Dixon finds a package that exposes him to a deadly pathogen. Marshall seems to be the only one who can help Sydney when she finds herself buried alive in a grave.
Sydney and Vaughn put themselves at risk to optain information regarding a project called "Nightingale. But they are unaware that they are being helped to find the project by Jack and Sloan.
Sydney's aunt, Katya Derevko, has devestating news for her about Irina's death. Vaughn acts as a rogue agent, stealing a device to use as a baragining chip for information about his father. Marshall has questions about Jack's health.
Sydney and Sloane team up to capture his impersonator. But when they learn what the imposter was after, Nadia fears her father will rediscover an old obsession.
Sydney and Nadia find Sophia, the woman who raised Nadia, viciously beaten. Sloane fears for Nadia's life when he learns why this has happened. Dixon faces a major moral dilemma while on a mission with Vaughn. Dr. Liddell has so advice for Jack.
While Sophia continues to regain her strength at Sydney's apartment, Sydney is horrified to discover Jack has been keeping his terminal illness a secret from her.
Sloanes impersonator resurfaces and sets his sights on the Rambaldi artifacts. Meanwhile, shocking revealations about the real Sloane are brought to light.
Invaders raid the DSR and make off with Rambaldi artifacts. It was because Nadia's computer was disabled that the raid was able to take place, and Jack and Sloane suspect that this is Sophia's doing, and that she is actually Irina Derevko. They follow her trail to a dead Rambaldi follower and a person they did not expect to find alive.
The Rambaldi endgame begins with a giant version of Circumfrence floating over a Russian city and driving the people there mad. An injured Dixon reveals Irina is alive, so Sydney and the rest set off to rescue. They learn she was working to prevent Elena and the Covenant from making the Rambaldi Prophecies come true. After the rescue, they set off to face Irina.
Sydney, Jack, Irina, Vaughn, and Nadia attempt to save the world from Elena Derevko's plot. The Rambaldi prophecy regarding Sydney and Nadia becomes closer to being true.