Season 2: Episode 14 - "Double Agent"
 

CIA Agent Jim Lennox is in bed with his partner, Emma Wallace. She tells him that she'd like to go back to Fiji. He agrees and they kiss. When he goes into the shower, she frantically types an email: "Abort operation. Lennox is a …" Lennox hits her before she completes the message. Sloane, whom Lennox has called to say he'd been compromised, tells him to make it public. Wallace, strapped with C-4, is thrown from a van onto a Berlin street.

In L.A., Vaughn tells Syd that Marshall and Dixon are being debriefed and Sloane is now on Interpol's most wanted list. He also tells her that he broke up with Alice. Weiss introduces Christine Phillips, a new clandestine services grad from Langley who will observe for the next few months. They all watch as Wallace appears on the news singing "Pop Goes the Weasel." The agents watch in horror as Lennox remotely detonates the C-4, killing Wallace.

Shortly thereafter Kendall briefs the staff, saying that Wallace's mission had been to gain the trust of Dr. Enzo Markovic, a scientist developing a technology known as Helix, to determine if it was a weapon. Enzo was believed to have gone to a secret lab in the Serena del Sol Resort in Cayo Cancho, off the Dominican Republic. Lennox is believed to be held there or dead. Sydney and Vaughn's mission is to acquire intelligence and bring Lennox back home.

Vaughn picks up Syd at her apartment. They kiss and she introduces him to Francie, who thinks they're going to a finance conference in New York. Syd gets a strange vibe from her.

At the resort, they force Enzo's security chief to reveal Lennox's location. Syd interrupts Lennox's torture and beats his two inquisitors. His eyes were affected so she blindfolds him and leads him away while Vaughn acquires the Helix files. When Syd is attacked by a guard, Lennox removes the bandage, risking his eyesight, to shoot him. Back home, the CIA gives Lennox a clean bill of health.

Under questioning, Lennox explains that while he and Wallace were working for Enzo as freelance security experts, the discovered that he was working for someone else. Lennox was going to hack the database in Cayo and transmit the data to Wallace in Berlin, but he was caught before that could happen. Sydney is shaken when he also reveals that he and Wallace were engaged.

Phillips analyzes the tape of Wallace's death and, due to static on the tape, determines that the detonator was within a block of the explosion.A sympathetic Syd visits the grieving Lennox at a safe house. He kisses her, but quickly apologizes.Two men appear and accost Lennox. He beats them but then Syd subdues him because the men are government agents who want to take Lennox into federal custody.

At the CIA, Jack reports that Helix is a new gene therapy that can reshape a patient's face and body. The only way to determine an actual identity is through an ocular scan — this flaw was purposely built into the procedure. Lennox, he says, was the first test subject to be doubled, meaning Lennox may actually be Enzo. Vaughn then places Lennox at the scene of Wallace's murder. Syd is dubious, believing Lennox's grief to be authentic.

Lennox's scan checks out okay, and he's shocked when Syd tells him he's been doubled. They learn that Enzo brought Helix to Poland. Syd and Lennox are to find it, download the schematics and destroy it.

At a railroad depot, they disable the guards and break into the freight car where the technology is hidden. Lennox reads data and learns that another person has been doubled. Vaughn receives a frantic call from a man claiming to be Lennox, who says the man the CIA rescued is really Enzo. This Lennox says the ocular scan is merely disinformation and that he's approaching the freight car and will destroy the technology.

Vaughn notifies Syd of the predicament. Jack tells her to disarm both men and they'll figure out the mess once they're both in custody. She makes Lennox handcuff himself to the freight car. When she leaves, he breaks his hand in order to slip through the cuff and picks up a gun.

Syd confronts the second Lennox, but the first one appears. They're in a standoff. Syd threatens to detonate Helix. The second Lennox reacts and tries to shoot Sydney. The first — and real — Lennox shoots and kills the phony. Sydney destroys Helix.

At the CIA, Lennox prepares to go to Fiji — he's never been there; he and Emma were going to go on their honeymoon. Later on in Syd's apartment, she and Vaughn fall into bed. But they're being observed through a camera secretly installed in the television. Francie watches — she's the other double.