When Sloane advises that Prophet Five send someone to intercept, Peyton introduces Anna - now Sydney's doppelganger. Sloane briefs her but comments that she's hardly Sydney and reminds her that she's dispensable. As Anna leaves, Sloane has a vision of Nadia, who tells him that he's just as dispensable.

At APO, Tom decodes a message hidden in a magazine. Rachel, feeling insecure, interrupts him. Tom assures her that she's a good agent.

Anna arrives in Nepal and deceives an escort expecting to meet Sydney. He tells her that Vaughn is excited to see her and his hideout is just a few minutes away. She kills him and gives his distinctive scarf to an accomplice.

Marshall discovers that the whole APO office is bugged. He meets Jack at a parking lot and shares the news that Sloane have placed the office on passive surveillance. They conclude that Sloane must have installed a backdoor access to APO's security system before his rights had been revoked.

Sydney arrives at the airport and is picked up by Anna's accomplice. Jack phones and informs her of the security breach and the possible intercept. When the impostor suggests that they help a stranded stranger, Sydney elbows him and tries to grab the wheel. The stranger fires gunshots at them and the jeep veers off the road and into a ravine.

Trapped under the jeep, Sydney watches as Anna takes the chip from her backpack. Anna says she's going to pay Vaughn a visit and sets the jeep on fire. Sydney escapes in time.

In Zurich, Sloane tells Peyton that Rambaldi was influenced by a 14th century cleric named Joseph Pinara and that he needs Pinara's manuscript to help him decode Page 47. He directs Peyton to a private bookseller in Geneva. When she retrieves the book, the clerk calls a superior and reports that someone is trying to make contact with him.

Anna arrives in Vaughn's hideout and tells him about the chip. Vaughn points to a scar on his shoulder, and says his father told him was from a bike accident. He lets Anna open the scar. Embedded is another chip with Renee's name on it. Combining the microchips together, they input the data in a computer and discover a map pointing to a Hamburg bunker. Vaughn suggests going with Anna, who immediately calls for transportation. Sydney arrives in Vaughn's hut to see the helicopter depart.

In the APO office, Jack tells the team that Vaughn is alive. He shows them a photo of Vaughn and Anna at the Hamburg airport, and says that he's with Sydney's clone.

Anna and Vaughn stake out a jewellery store near the bunker. When Vaughn suggests they do what they did in Cartagena, Anna says she'll follow his lead. Anna holds up the shop owner as Vaughn enters the bunker. As he picks up a file, Anna arrives and points a gun at Vaughn. She pulls the trigger -- but Vaughn had taken out the clip. They fight. Vaughn, weakened from his seclusion, falls first. As Anna is about to kill Vaughn, Sydney arrives and shoots Anna dead.

In Zurich, Sloane tells Peyton that he needs to make peace with the past. He goes to a church with a Prophet Five guard and leaves a matchbook by the candles. As he leaves, Sark arrives to pick up Sloane's message.

Syd and Vaughn realise that files contain Vaughn's father's research on Prophet Five. When Anna's phone rings, Syd answers. Pretending to be Anna, she sets a meeting with Peyton. Before Sydney leaves, she embraces Vaughn and says goodbye once again. Later, Syd, posing as Anna posing as Syd, hops in the car with Peyton and hands her Renee's microchip.