An elevator falls 40 stories, killing the three men inside. Sark pries open the door and retrieves a wallet from one of them, a Russian arms dealer named Yuri Karpachev. At a briefing, Kendall tells Jack that Karpachev was one of Irina's contacts. Jack also knows that Karpachev had ties to Sloane.

Irina tells Jack that Karpachev's wallet contained a key to his safe, which Sloane believes contains a Rambaldi manuscript. It doesn't, she says. Karpachev sold it to a man in Bangkok named Ilya Shtuka. She proposes a meeting with Shtuka to obtain the manuscript. Word of her re-appearance would also draw out Sloane. If he's captured, Irina hopes, then Sydney will quit the CIA.

Sydney is called in to meet with Mitchell Yager, a counter-intelligence analyst who is investigating Vaughn. Vaughn, he says, has contacted unapproved foreign operatives and met with Vladimir Prokrowski, a former KGB assassin. He pressures Syd to examine Vaughn's laptop because he may have downloaded a forbidden decryption program called Xenon. .

Meanwhile, Kendall is hesitant to allow Irina to make contact with Sloane. Jack reassures him, stating that he'll escort her, and that they'll bait Sloane with the manuscript. He says that he'd know if Irina was deceiving him again. Marshall implants a tracking device in Irina's shoulder.

Irina meets with Shtuka at a Bangkok nightclub. He reveals that traded the manuscript for opium rights in Hong Kong. Irina kills him, and is then saved from an attacking thug by Jack. They fly to Hong Kong, where they manage to obtain the manuscript.
At the CIA, Vaughn calms a suspicious Syd, who then returns to Yager and states she can't betray someone she loves.

Sloane is informed of Irina's appearance and requests a meeting in Panama to discuss the purchase of the manuscript. Jack and Irina will be accompanied by a delta force. Irina requests a visit from Syd, and tells her that the mission is going to be dangerous — and that she loves her.

At the apartment Francie puts Will under hypnosis, and he reveals the orbital location of a satellite, as well as its operational controls.

In Panama, Irina and two guards are to meet Sloane. They'll be tracked by a CIA satellite — when the time is right, the delta team will ambush Sloane. At Irina's behest, Jack removes the tracking device so Sloane cannot possibly detect it. Jack and Irina kiss.

      Weiss tells Syd that Vaughn is about to be charged. They locate Vaughn at a bar, where she observes him secretly receiving a package. She confronts him, telling him the CIA suspects he's a spy. Vaughn confesses to Sydney that he's been investigating Irina since she turned herself in. After months of research, he's found nothing to suspect she has an agenda.

Expecting Sloane, Irina finds only Sark, who has arrived in a limousine. She and the guards cautiously enter. The CIA loses the satellite signal — it's been hacked by Sloane, based on the info that Will had given Francie. Subsequently, Jack tells Kendall that he cannot activate the tracking device, and to send in the Delta team. The team surrounds the limo at a pier but the occupants are not Sark and Irina. It's a dupe that was used when Sark drove through a tunnel. Kendall checks the manuscript at the CIA and finds that it is filled with post-it notes.

Sark stops his car under a bridge, shoots the two guards and tells Irina to get out. A van arrives with Sloane inside. Irina thanks Sloane for extracting her, and hands him the manuscript, which she had hidden with her during the entire operation.