Sydney quits the CIA, and joins a Black Ops unit, Authoried Personnel Only, along with Vaughn, Dixon, Jack, and Sloane. Meanwhile, what Sydney found out in Wittenburg may endanger her relationship with Jack.

Sydney teams up with Jack, unwillingly, to hunt down a criminal, who is a modern day Samuri. Meanwhile, Nadia wants to go back home, but is forced to join the CIA when Sydney's life becomes endangered. Sydney finds out the reasons behind Jack's misdeed.

Sydney is forced to seduce an arms dealer in order to obtain a NSA code-breaker. Also, Sydney and Jack fight to tell Nadia about Irina. And Vaughn fears for Weiss' life.

Sydney and Vaughn go undercover to obtain a deadly bio-weapon. Meanwhile, Nadia goes to Jack to find out more about Irina. Also, Sydney becomes worried that Vaughn has not gotten over Lauren.

Sydney and Vaughn go undercover as a married couple to find a weapon, but soon realize that the town which they are in, is not what it seemed.

Sydney starts to lose touch of the world when she gets altered by hallucinogen, and Jack and Vaughn look for a cure, before she strts to put her and the ones she loves in danger.

Sydney and Nadia argue over Sloane's new behavior, fatherly behavior. Meanwhile, Sloane worries when Nadia and Sydney's mission turns wrong when they disobey the orders.

Jack temporarily takes over as director, when Sloane steps down, over their ext mission, which includes Anna Espinosa, Sydney's old enemy. When Anna kidnaps Nadia, she forces Sydney to do what she wants. Sydney tells Nadia about Rambaldi's profecy saying about two sisters fighting but only 1 surviving. Also, Vaughn goes to Sark to helps.

Sark is taken to APO to help them retrieve a bomb from Cadmus Revolutionary Front, but he says that the only way he wll help is if he is allowed to see Laurens body, which Vaughn unwillingly accepts. Nadia is the only one able to with the knowledge to retrieve the bomb, but unfortuately she is still in a coma. Jack is forced to bring her out of her coma, which may not be safe.

Sydney and Dixon try to prove that Sloane is double crossing the CIA by by using APO to take the Blackwell Index, and is trying to reconstruct the Alliance. Sydney inspects Sloane's house, but when Nadia finds out, she isn't too happy. Meanwhile, Vaughn finds out news about his father, when he visits his uncle.

Sydney is forced to protect a bartender she met, after she accidentally puts him in danger. Meanwhile, Vaughn finds out more about his father, and Jack visits an old friend.

Nadia puts the one's she loves lives in danger when she forgets to tell them about her criminal past. Meanwhile, Vaughn meets a woman who knows Nadia as well.

When a mission does not go well, Sydney is attacked and her life is placed in danger. The only one who can save Sydney is Marshall. Meanwhile, Dixon is infected with a deadly pathogen during a CIA lockdown.

Sydney and Vaughn go undercover to find out about Vaughn's father.

Katya Derevko purposefully poisons herself, in order to talk to Sydney, and is temporarily removed from her cell. When Sydney finds out that Nadia has been visiting Katya, she goes to visit Katya, and warns her not to talk to her sister again. But when she arrives there, Katya tells her that someone framed her mother to get her killed. Sydney goes looking for some answers. Meanwhile, helps out another agency to find out more information about his father. In the end, they both find out the same man was behind everything...Arvin Sloane.

Vaughn and Sydney tell Jack about Sloane's involvement with Vaughn's father, and Irina's contact, but after talking with him, they find out that someone is framing Sloane. Soon they realize that the other Sloane is a clone, and Sloane decides it's best to step down, but Sydney disagrees. She says that it will be best because he knows exactly what the new Sloane will do, but Nadia is fearful that in her father's hunt to capture the new Sloane, he'll start to become obsessed again with Rembaldi.

Sophia, Nadia's old caretaker, contacts Nadia, after being severly beaten. Sophia tells Sloane that she was beaten up because someone was after Nadia, so him and Jack decide to tell their daughters the truth, that Elena Derevko has been watching both of them for a decade. Also, JAck's doctor advises him to tell Sydney about his sickness.

Jack’s sickness makes him hallucinate about an antidote. Also, Sydney is forced to pretend to be her mother, so that she can recreate the time when Jack was working was for the CIA.

They capture the Sloane imposter question him about the Rambaldi orchird, but first the real Sloane must remember a painful memory, so that the fake Sloane will reveal where it is.

When a group enters the DSR and steals the Rambaldi artifacts, Hayden CHase, CIA director, finds out that the alarms were disabled from Nadia's computer, and take her in for questioning. Afterwards, Jack and Sloane suspect Sophia, who is living with them, is Irina's sister, Elena Derevko.

A giant version of the Circumference/Mueller device is found floating over city in Russia, making the citizens insane, as Rambaldi's plan begins. Sydney, Nadia, and Jack search for Irina after Dixon finds out that she was still alive. They find out that Irina had been kidnapped and cloned, to make it seem like she was dead. Sydney and Nadia find her in a camp in Tikal, captured by Elena's army. Irina had been captured, because she was working against Elena to stop Rambaldi's endgame. She was forced to recreate it, and now Jack, Sydney, Vaughn, Nadia and Irina need to go to Russia to stop it. Also, Vaughn has a surprise for Sydney.

Jack, Sydney, Vaughn, and Irina parachute into Sovogda, trying to dismantle a giant red ball turning people into zombies. Meanwhile, at APO, Weiss and Marshall blackmail the Russian Minister to access the Russian satellite codes, which leads them to learning that Elena Derevko is uplinking the satallite. Now, Jack, Sydney, Vaughn, and Irina have to save Nadia, and stop Elena and Sloane.