The fourth season opens with a flashback from a scene of Sydney in hand-to-hand combat on a moving train. We learn that she is on a mission to recover an isotope with a fantastic name. Sydney and Vaughn reconcile passionately after their brush with death. The plot leads directly into a second hour titled Authorized Personnel Only: Part 2.

International titles

• German: Authorized Personnel Only, Teil 1 (Authorized Personnel Only, Part 1)
• French: Jeu d'espions, première partie (Spy games, part 1)
• Polish: Tylko dla twoich oczu I (For your eyes only I)

Following the theft and delivery of an ancient sword, Sydney learns that her father had her mother executed to prevent a hitman from assassinating her. Sydney, Jack, Vaughn, Dixon, Marshall, and Nadia are recruited into a "legitimate SD-6" black ops division of the CIA dubbed "APO" (Authorized Personnel Only). The new division is headed by alleged "former villain" Arvin Sloane.

Note

• This was J. J. Abrams's last script for the series.

International titles

• German: Authorized Personnel Only, Teil 2 (Authorized Personnel Only, Part 2)
• French: Jeu d'espions, deuxième partie (Spy games, part 2)
• Polish: Tylko dla twoich oczu II (For your eyes only II)

Sydney seduces an arms dealer in order to locate a stolen National Security Agency code-breaking device. Team members rescue each other and Sydney and Jack argue about telling Nadia the truth about her mother's death. Jack manipulates Nadia into killing someone by leading her to believe that the person killed her mother.

Note

• During Weiss' birthday party, Jack Bristow visits Sydney. The song playing at the party in the background is "You All Everybody" by DriveShaft, the fictional band of Charlie Pace from J. J. Abrams's new series, Lost.

International titles

• French: Cruelle vérité (Painful truth)
• German: Furchtbare Wahrheit (Awful truth)
• Polish: Okrutna prawda (Awful truth)

Vaughn goes undercover as a priest with a dark past. He and Sydney set out to intercept a bioweapon called Ice Five, similar to the Ice Nine in Kurt Vonnegut's novel Cat's Cradle (it causes the water in the body to crystallize instantly at room temperature). Vaughn still feels guilty over Lauren's death; he confesses his feelings with a sympathetic enemy and he bonds with her. Nadia has questions for Jack regarding her mother, Irina Derevko.

International titles

• German: Ice
• French: Cryo 5
• Polish: Zamrożeni (Frozen)

Posing as Russian nationals, Vaughn and Sydney are brought to a "village" located in Russia that resembles a typical American town. It was once used to train KGB agents in how to blend into American society, but is now being used by a terrorist cell to train operatives in preparation for bringing down America's economy using an electromagnetic pulse weapon. Marshall discovers information in a book Irina Derevko used to contact her handlers. For some reason, some Russian group is trying to find Derevko.

• This episode strongly resembles an episode of Danger Man titled "Colony Three" in which John Drake infiltrates a Russian facility that simulates a British town. It also resembles an episode of Mission: Impossible titled "The Carriers" where the team headed by Dan Briggs poses as foreign agents being trained as U.S. citizens in a simulated Illinois town so that they will unknowingly carry a plague to America.

International titles

• German: Willkommen in Liberty Village (Welcome to Liberty Village)
• French: Le village (The village)
• Polish: Szpiedzy gotowi na wszystko (Spies ready for anything)

Sydney comes in contact with an infectious drug and suffers deadly hallucinations. Dixon tells Arvin Sloane he suspects him of having a treacherous endgame and threatens to kill him when the time comes.

International titles

• German: Nocturne
• French: Confusion mentale (Mental confusion)
• Polish: Antidotum (An antidote)

Sydney expresses her full hatred for Sloane during a mission to intercept a cache of an extremely powerful explosive called Black Thorine.

International titles

• German: Explosiv (Explosive)
• French: Thorine noire (Black Thorine)
• Polish: Jak dwie krople... (Like two peas in...)

Former K Directorate agent Anna Espinosa abducts and tortures Nadia. Sydney relates a Rambaldi prophecy that says that she and her sister must fight to the death. Sloane makes it clear that Espinosa is part of the Cadmus Revolutionary Front; a Rambaldi-obsessed group and will try to make the prophecy come true. Espinosa shoots Nadia, leaving her in a coma. Mr. Sark claims to have knowledge about the Cadmus Revolutionary Front and tries to cut a deal.

International titles

• German: Echos (Echoes)
• French: Face à face (Confrontation)
• Polish: Żyje się tylko trzy razy (You only live three times)

Espinosa's bomb is assembled and ready for sale. Sark claims to be a man of his word and helps Sydney capture Espinosa while securing his own escape. Jack wakes Nadia prematurely to gain intel on the Cadmus Revolutionary Front. When Sloane confronts him, Jack claims to be a man of his word as well.

Notes

• Melissa George makes an uncredited cameo as Lauren Reed.

International titles

• German: Ein Mann ein Wort (A man a Word)
• French: Dernier recours (Last resort)
• Polish: Człowiek honoru (A man of honour)

Sydney uses Nadia's birthday dinner as a pretext for stealing the key to Sloane's secure phone. Sydney and Dixon learn that Sloane has contacted old Alliance associates. The two conspire to give the CIA a corrupted key to an encrypted database—a master blackmail list. When Sloane arranges a meeting with his old associates, Jack presents them with the key to The Index. Jack is pistol-whipped when the key does not work. Nadia rescues him. Jack and Sloane finally gain access to the list. Vaughn receives a mysterious package from a mysterious 'fake nurse' while visiting his comatose uncle in the hospital. It contains a key that leads him to a journal written by his "late" father, which contains entries after the date of Vaughn's father's alleged death.

International titles

• German: Index
• French: Intime conviction (Private conviction)
• Polish: Indeks (Index)

Jack kills an old friend who is poised to receive a biometrically targeted weapon. Sydney confronts the weapon (miniature helicopter with automatic weapons fire and Artificial Intelligence) and saves an innocent civilian. Vaughn learns that his father was possibly a traitor.

International titles

• German: Kein Entrinnen (No Escape)
• French: Service commande (Order department)
• Polish: Droga do domu (The road home)

Nadia's orphan past, her recruitment and her recruiter's treacherous background are revealed. In a search for his father, Vaughn meets up with none other than the headmistress of Nadia's orphanage in Argentina. Vaughn asks her if she remembers anything out of the ordinary when his father stayed at the orphanage, which she replied she said she heard him say something about "Nightingale". She asks about Nadia, also.

Note

• Sônia Braga guest stars as Sophia Vargas.

International titles

• German: Dunkle Vergangenheit (Dark Past)
• French: Cicatrices intérieures (Inner scars)
• Polish: Sierociniec (Orphanage)

The episode begins in Havana. Sydney rendezvous an informant by dancing with him. The information he gives is relayed to Dixon and leads to the recovery of a hard drive from a locker. Later, Sydney's taxi driver is shot and she is captured by the informant's boss. The informant is shot in the head and Sydney is subsequently buried alive in a coffin, in the middle of a graveyard.

The hard drive turns out to have been booby-trapped by Third Faction. When inspected it detonates and releases cyclosarin. The biological nerve agent infects Dixon as he attempted to aid the technician who was inspecting the hard drive. Due to the release of the nerve agent, APO goes into lockdown mode for thirty-six hours.

Marshall, late for work, arrives at the parking lot only to be informed that they're in lockdown mode and that Sydney is trapped in a coffin somewhere in Cuba. Sydney is able to communicate with her cell phone that she still had. Because Marshall is the only one not affected by the lockdown, he volunteers to go to Havana to find the graveyard where Sydney is buried; using a transceiver he rigged to locate her cell phone and re-tasking a thermal imaging satellite, Marshall finds Sydney unconscious, but alive. Marshall and Sydney's mission is extended to Berlin where the man who gave them the phony hard drive is located. Since the man knows what Sydney looks like, Marshall is sent in to get a copy of the data using a remote scanner. Marshall accidentally shoots and kills him. Over the phone, Jack instructs Marshall on how to remove the man's eyes (using a spork) so that he can access a security station in the basement and deactivate a firewall. After doing so, Sydney and Marshall rendezvous and finally obtain a real copy of the hard drive, which they deliver to APO.

In the middle of it all, Marshall must sing his baby to sleep by phone with a song about the Lanthanide series. Though his wife is an NSA employee, he can never tell her where he has been.

International titles

• German: Dienstag (Tuesday)
• French: Le fantôme (The ghost)
• Polish: Sześć stóp pod ziemią (Six feet under the earth)

While searching for Vaughn's father, Vaughn and Sydney discover that Nightingale is a molecular weapons system located in a nuclear reactor in Siberia. Sloane and Jack know about Nightingale and its connection to Elena Derevko. The duo later use Sydney to have Vaughn bring the information to APO and thus make it an official mission.

Meanwhile, a mysterious stranger meets with Vaughn in the UCLA library and promises answers about his father in exchange for the Nightingale's coil. Vaughn, Sydney and Jack travel to the Nightingale facility to shut it down and retrieve the coil from the weapon, however, Sydney becomes trapped in the room with the Nightingale device. Jack, Vaughn and Marshall attempt from three different locations to free her, which ultimately leads to Jack shutting down the nuclear core manually exposing himself to harmful radiation. With Sydney's help, Vaughn disappears with the coil to learn more of his father. Marshall later discovers what Jack did, but swears to keep Jack's secret.

International titles

• French: Contre-mission (Countermission)
• German: Nachtigall (Nightingale)
• Polish: Kryptonim słowik (Code name: Nightingale)

Vaughn makes an agreement with the mysterious man he met in the episode "Nightingale", to intercept a CIA shipment of a Rambaldi manual in exchange for information on his father, Bill Vaughn. In the process, Vaughn is forced to shoot Dixon to ensure the success of the mission.

Meanwhile, Nadia informs Sydney that she's been secretly seeing Katya Derevko. When Sydney confronts Katya, she learns that Irina did not put a contract on Sydney's life at all. Sydney tracks down a message from her mother that has been hidden inside a music box. The message is the number to a bank account under the name of Arvin Sloane.

Marshall dupes Jack into signing some papers, which Marshall uses to test Jack for mutations due to his radiation exposure. The test returns positive and Marshall confronts Jack informing him of the effects this may have to people who care about him, such as Sydney if she found out, unless he goes to a doctor.

Vaughn, after the success of the mission, learns that his father has actually been dead all this time and that everything, including the journal was forged supposedly by Sloane. Later, Jack reports to Arvin Sloane that Vaughn has returned with the Nightingale coil and that the CIA was still in possession of the Rambaldi artifact. It was also mentioned that Dixon was merely shot in his vest and would eventually recover.

During the final moments of the show, a second man referred to as "Mister Sloane", and bearing a distinct resemblance is revealed in Santiago.

Note

• Joel Grey guest stars as "Arvin Clone."

International titles

• German: Pandora
• French: Haute voltige (Acrobatics)
• Polish: Pozytywka Pandory (Pandora's music box)

A physicist specializing in Quantum Electrodynamics is abducted in Kraków. In custody, Roberts, the mysterious man makes contact with "Marvin Sloane's" second in command to arrange a meeting to deliver the coil vital to what the impostor Sloane is building, but the meeting goes awry and the coil is stolen. Sloane convinces all that an impostor is responsible for the recent activities. After promising Nadia that he is trust-worthy, Sloane is allowed into DSR to examine the Rambaldi artifacts to determine the impostor's next move. Sloane loses it during the recovery mission and bludgeons a man to death for assuming that the Rambaldi technology is related to eternal life. The impostor escapes, but his power source (an immense sphere seen in the season 1 episode "Almost 30 Years") remains. This episode make mention of a fictional chemical element, Zanthium 242.

Note

• Joel Grey guest stars as "Arvin Clone."

International titles

• French: Sloane et Sloane (Sloane and Sloane)
• German: Zweites Ich (Alter ego)
• Polish: Drugi Sloane (The second Sloane)

Jack seeks a doctor who might be able to cure his radiation poisoning, but the doctor cannot help him and tells Jack that he must tell Sydney. Sophia, Nadia's caretaker when she was young, calls her and she comes to Los Angeles. She reveals that she was beaten when someone came to look for Nadia. Meanwhile, Vaughn and Dixon go on a mission in Amsterdam to find an agent who might have gone rogue. Dixon's associate is actually pursuing leads on Hydrosek, a water-based weapon developed by Indonesia that could wipe out entire ecosystems and kill millions. Sloane (via Marshall) acquires intel on Sophia just to be sure she was telling the truth, but Sydney finds out. Jack and Sloane later confess that they know that someone has been watching Sydney and Nadia since they were young and acquiring information about them. It is revealed that Elena Derevko is the one who has been accumulating the information. It is then shown that Sophia and Elena are one and the same.

Notes

• Sônia Braga guest stars as Elena Derevko.
• Michael McKean guest stars as Dr Liddell.

International titles

• German: Reines Gewissen (Clear Conscience)
• French: En sursis (Reprieve)
• Polish: Czystka (The purge)

Jack has been hallucinating visits with Dr. Atticus Liddell, a man that Jack helped relocate in 1981. Liddell specialized in radiation therapy and is believed to be the only man capable of improving Jack's health, only no one knows where Dr. Liddell is except for Jack. When Jack wakes up in a hospital, he thinks Sydney is his ex-wife, Laura. Sloane then asks Sydney to pose as her mother to get information from Jack that will lead to where Dr. Liddell is hiding. A fake house is set up and re-created to look like his former house in 1981. He reveals openly to "Laura" that he was relocating Liddell to Helsinki. Sydney subsequently finds him and brings him to APO to help Jack.

Elena steals the Hydrosek recovered earlier and kills her ally after the heist.

Notes

• Sônia Braga guest stars as Sophia Vargas.
• Michael McKean guest stars as Dr Liddell.

International titles

• German: Trugbild (Mirage)
• French: Rêve empoisonné (Poisoned dream)
• Polish: Powrót do przeszłości (Return to the past)

"Arvin Clone" raids a monastery for a Rambaldi orchid from which an anti-aggression drug can be made, one which his power source, the Mueller Device, can reverse. In CIA custody he displays Sloane's memories. He is the product of an SD-6 Psych-ops specialist's experiment. Sloane contaminated world water supplies when he was with OmniFam, and with the orchid, the "clone's" employer can render hundreds of millions passive, finishing what Sloane failed to do. The team decides to break the imposter by imprinting him with Sloan's most painful memory—the very thing that sparked his Rambaldi obsession. Sloane re-visits in his memory his dead wife, Emily, and the time when his baby, Jacquelyn, died. Arvin Sloane must decide whether to return to Nadia and repair the damage he has done to the world or live in a dream.

Notes

• Amy Irving guest stars as Emily Sloane.
• Joel Grey guest stars as "Arvin Clone"/Ned Bolger.
• This was Jennifer Garner's directorial debut, and the only episode of the series to be directed by a member of the cast.

International titles

• German: Wer bin ich (Who am I)
• Polish: Jak we śnie (In a dream)

Elena Derevko raids the DSR facility holding all the CIA's Rambaldi devices. The CIA traces the conspiracy back to Nadia's laptop and the bugged necklace Sophia Vargas (who was Elena Derevko all along) gave her. In a flashback Arvin Sloane and Nadia Santos visit the one man who knows how to assemble the Rambaldi device. The man is subsequently killed by Elena. When Sloane and Sydney arrive at the man's trailer they find him murdered. Sloane then betrays the CIA by knocking Sydney out and fleeing with the knowledge of Elena's location. Since Sloane is the only living expert on Rambaldi, they join forces.

To find Elena and Sloane, Jack Bristow visits Katya Derevko and promises her immunity for information on Elena's whereabouts which she then gives to Jack. Dixon, Nadia, and Sydney then infiltrate Elena's compound, where Dixon is shot by Elena, but not before positively identifying that Irina Derevko, long thought to be executed by Jack, is still alive.

Notes

• Sônia Braga guest stars as Elena Derevko.
• Isabella Rossellini guest stars as Katya Derevko.

International titles

• German: Abstieg (Descent)
• French: De Charybde... (From the frying pan...)
• Polish: Upadek (Collapse)

The episode begins with a flashback in which Jack executes Irina 18 months prior. It was, however, not Irina who was killed and instead a double from the Project Helix. It is learned that Irina's death was an elaborate setup by Elena Derevko in which Jack was meant to execute the double to make everyone believe she was dead. The information on the double is confirmed through an encrypted file called the Blackwell File (retrieved in an earlier episode). With the knowledge that Irina was still alive, Jack, Sydney, and Nadia stage a search and rescue in Guatemala where Irina was being held.

While all this is going on, a device known as the Mueller Device (Marshall calls it the Big Red Ball) is put into place over Sovogda, Russia, the entire population of which is rioting much like the frenzied bees from In Dreams.... The Rambaldi prophecy appears to be coming true and only Irina has the knowledge to foil Elena and Sloane's plot. The team makes a HALO jump into Sovogda in an attempt to shut down the Mueller Device. The Russian authorities have ordered an airstrike, but since rupturing the sphere would release a vast amount of toxins, time is running out.

Note

• Lena Olin guest stars as Irina Derevko.

International titles

• German: Befreiung (Rescue)
• French: ...en Scylla (...into the fire)
• Polish: Misja ratunkowa (A rescue mission)

The team parachutes into Sovogda, where they find that most of the citizens are dead. The Mueller device is floating over the tallest building, where Elena and Sloane are currently carrying out Part One of Rambaldi's endgame. The Russian Air Force will soon launch an air strike, which is when Elena will activate the signal and transmit the Rambaldi signal worldwide with deadly ramifications as global water supplies are already primed. A strike would also release deadly radiation into the atmosphere and make Chernobyl look pale in comparison — in Jack Bristow's words, "like a kitchen fire."

Sloane "betrays" Elena and leads the team to her. She is then captured and Irina makes her tell her which wire to cut on the device to deactivate it. Elena says to cut the white wire, but Irina tells Sydney to cut the blue wire. Irina then shoots Elena, killing her.

Nadia becomes infected when Elena injects her with the infected tap water, who tries to kill Sydney to prevent her from stopping the device. Sloane shoots Nadia to save Sydney's life in fulfillment of the prophecy. The Mueller device then dissolves into water and destroys the building, but the team makes it out. Jack then lets Irina go free.

The end of the episode shows Sydney and Vaughn in a car going off on vacation to Santa Barbara, where they decide they would elope. After being prompted by Irina of not having a marriage full of lies like her marriage with Jack, Vaughn tells Sydney that he doesn't want to keep any secrets from her. As they're driving he tells her his real name isn't Michael Vaughn and that his assignment of being Sydney's handler was no accident; however, before an explanation can be given, their car is hit in the driver's side door by another vehicle.

Note

• Sônia Braga guest stars as Elena Derevko.
• Lena Olin guest stars as Irina Derevko.

International titles

• French: Il Diluvio
• German: Vor der Flut (Before the flood)
• Polish: Proroctwo (The prophecy)