Episode 15: Pandora
Dixon is shot by a masked gunman. The shooter approaches and takes off his mask, revealing … Vaughn.
Two days earlier, Vaughn meets a man named Roberts in a Paris cafe. Vaughn tells him that Roberts' employer will only get the transformer coil if they give more information about Bill Vaughn first. Roberts calls his employer and has him speak to Vaughn. The voice says that since Vaughn didn't follow their agreement, he must first complete an assignment. As instructed, Vaughn reaches under their table and opens an envelope containing surveillance pictures of Bill Vaughn, who, the voice confirms, is very much alive.
At a federal prison, Nadia visits Katya Derevko, who fondly recalls her childhood with Irina. Nadia refuses to talk about Syd, although Katya desperately wants to see her.
Concerned about Jack's exposure to radiation in the last mission, Marshall secretly uses the oil from Jack's fingerprints to create a sample that he sends to forensics for analysis. Later, Marshall learns that the results show a large-scale genetic mutation. He begs Jack to see a doctor.
Vaughn meets with a group of freelancers hired for the assignment. Roberts announces that they must steal a valuable item from an armored van - but first, they need a cold laser stored in a private hospital at Bordeaux. Vaughn and a team member infiltrate the hospital, first disguised as a couple needing medical attention, then as a doctor and a nurse. They successfully steal the laser.
After Nadia confesses to Sydney that she's been visiting Katya to learn more about Irina, Syd warns Nadia and reveals that Irina had hired an assassin to kill her. An angry Syd storms off to see Katya in the hospital.
Syd tells Katya to stay away from Nadia. Katya says that she would never harm Syd, nor would Irina. Before her death, Katya says, Irina believed that someone was setting her up to make it appear that she was trying to have Sydney killed. Katya gives Syd a lead.
Roberts briefs his team about their assignment: stealing a Rimbaldi manuscript from a CIA convoy. An angry Vaughn confronts Roberts, declaring that he can't betray his agency, and that if he did this, he can't go back. Roberts responds by saying "like father like son," and that his father was a bad guy himself.
Following Katya's suggestion, Syd goes to a repair shop and brings home a music box. Syd realizes that the box's flashing lights project a set of numbers, which Sydney researches in the CIA files. It leads to bank records containing payments to Syd's would-be assassin - whose source has the name "A. Sloane." Since it exonerates Irina, Syd shares this with Katya.
Vaughn and his partner infiltrate an armored van in the CIA convoy by burning a hole through the floor. Using the cold laser, they bypass security and secure the artifact. Vaughn runs out with his partner - but Dixon, who is part of the CIA convoy, chases them through a tunnel. Vaughn's partner shoots Dixon and Dixon fires back. Instinctively, Vaughn shoots Dixon. As Dixon slumps to the ground, Vaughn peels off his mask, realizing what he's done.
Vaughn meets Roberts at a warehouse and beats him silly. He demands the truth. Roberts admits that Bill Vaughn is dead, and that the journals and pictures were a set up. He says that he works for Sloane.
Vaughn arrives at Syd's apartment and they embrace. Vaughn says his father had been dead all along, and that he realized that the father he knew would never have walked away from the people he loved. Vaughn tells Sydney that Sloane was behind this.
In Santiago, Chile, a frustrated agent reports to his boss that Roberts failed and the manuscript has not been recovered - he calls his boss "Mr. Sloane." This Sloane, who resembles Arvin Sloane, tells him that everything should proceed as planned.
- description from ABC.com