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On a CIA mission, Sydney learns of a new development: a process that allows a person to be genetically doubled. She finds data that reveals two people have been doubled: a CIA Agent named Jim Lennox and an unknown second person.
The fake Francie plants listening devices and hidden cameras around Sydney's apartment. She also begins a relationship with Will, and she secretly obtains information about the CIA from him, using hypnosis.
Vaughn ends things with Alice. With SD-6 gone, he and Sydney begin an open relationship that frequently includes him staying over at her place. In a meaningful gesture, she offers to let him have a drawer in her bureau.
As Sydney considers quitting the CIA, Sloane phones her, offering his congratulations about her graduation from college. He tells her that he knew she and Jack were double agents, and he used them to free himself from the Alliance. Sydney realizes that her work is not done and she decides not to resign. She and the rest of the CIA search for answers when they learn that Sloane is still planning something that involves Rambaldi's work.
Dixon and Marshall are offered jobs at the CIA. Marshall joins and immediately thrives in his new position. Dixon is initially reluctant to accept because he's angry at Sydney for having lied to him. He soon overcomes his issues and comes aboard when he's needed.
With the objective of finding Sloane, Irina is allowed to leave her cell and accompany Jack on a mission. Irina met with Sark as planned, and he agreed to take her to Sloane. However, they were able to escape from the CIA. When it was discovered that Irina had taken one of the Rambaldi artifacts, Jack knew that Sloane and Irina had planned the whole thing.
In Tuscany, Emily discovered that Sloane was still not being honest with her because he was still up to something. Unwilling to live a life of deception anymore, Emily turned herself in to the local consulate, saying that she would only talk to Sydney. To say the least, Sydney was surprised to learn that Emily was alive; Sydney has given a speech at Emily's funeral, calling her the mother she wished she had. Emily agreed to reveal the location where Irina and Sloane would be, on the condition that Sloane not be harmed. Later, as the CIA surrounded their villa, Sloane was prepared to give up his quest and sell all of his assets to Irina for Emily's sake. Overcome by guilt, Emily told him that the CIA was outside. He said that it didn't matter, and she agreed to flee with him. However, as they ran from the CIA, Emily was killed when Dixon misfired. Sloane is heartbroken, but Irina manages to pull him away and they escape with Sark.
Sloane takes revenge on Dixon by murdering Dixon's wife, Diane. Vaughn becomes concerned after Dixon grows over-zealous in his efforts to find Sloane. Meanwhile, Sloane takes a trek to the Himalayas to confront the monk who sent him on the Rambaldi quest thirty years earlier; the monk tells him the journey has just begun as he allows Sloane to read what's written on a scroll.
When the CIA discovers a breach in their security system, the search for the culprit leads to Will when the fake Francie frames him as the second double.
Irina visits Syd, explaining that her plan was to deceive the CIA but she never lied about her feelings for Sydney - or for Jack. Irina provides information that proves Will isn't the double, but when the CIA follows another lead provided by Irina, they wind up raiding a warehouse full of fakes. Later, she swears that she didn't know that the Rambaldi artifacts had been moved.
In an ambush, Sloane captures Jack, as well as the artifact he was missing. He keeps Jack alive "because they're friends." He tells Jack that assembly of a Rambaldi device called The Telling is almost complete, and he speaks about a coming change.
The CIA learns where Sloane is and moves in. Sloane escapes, but Jack is rescued. Sydney finds Irina. Irina says that the Rambaldi prophecy refers to Sydney and that she is the one who can stop Sloane. Wishing Sydney luck, Irina escapes.
Meanwhile at Sydney's apartment, Will discovers that Francie is a fake. They fight briefly until she stabs him. Sydney later returns home, where Francie is sitting on the couch. Checking her messages, Sydney finds one that Will had left, telling her about Francie. The fake realizes that she's been discovered, and she and Sydney fight. Sydney finally reaches a gun and shoots Francie before passing out from exhaustion.
When she wakes up, she's in an alley in Hong Kong. She calls Kendall who directs her to one of their safehouses before asking her if she remembers where it is. At the safehouse, Sydney notices a scar on her abdomen. Vaughn arrives: he looks shocked to see her. She asks about Will and Francie, and Vaughn tells her that Will lived and that he's okay. Vaughn pauses, searching for what to say next. Sydney asks why he's wearing a ring. He tells her that they thought she was dead: she's been missing for over two years.
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