Sydney and Sloane leave the bank while Vaughn works to disarm the C-4 in the bank's basement. While Syd drives Sloane's getaway car, she tells him that he's on the CIA hit list. Sloane, having learned that the C-4 is disarmed, jumps from the car to a speeding van that eludes Sydney. Later at the CIA, Kendall and Syd argue about Sloane, with each saying the others efforts are sub par.

Vaughn receives a call from Weiss while at Sydney's apartment. The phone call triggers one of the hidden bugs, which replays a previous conversation. They locate the bug in a wall. At the CIA, Marshall says that he had made the bug while at SD-6. The bug, he says, periodically transmits to a receiver, which is why Vaughn heard it over his cellular. Jack orders Marshall to reverse engineer the bug to find to whom the conversations are going.

In Switzerland, as Sloane views a Rambaldi page with a hole in the center, Sark informs him that Caplan's tests are complete. The artifact is ready, and Sark will now prepare to test it. Sloane flies to Kandahar and meets Ahmad Kabir, a Pashtun warlord, hoping to recruit him as a partner in his nefarious plans. He wins over the reluctant Kabir with a gift — a pen once belonging to a 17th century Afghani warrior-poet.

At Syd's place, Francie tries to get Syd to talk, saying they've grown apart recently. But Syd receives a phone call from Vaughn and leaves immediately. Francie realizes that the bugs have been discovered and calls Sark, who tells her that they'll be looking for an L.A. asset so she should simply give them one. She later kills and frames Sydney's plumber.
The bug's feed proved to be untraceable, but Kendall has info placing Sloane with Kabir. In discussing a way into Kabir's compound, Sydney reveals that Dixon had infiltrated his operations and stolen a missile shipment. Kendall orders Sydney to recruit Dixon. She tries, but is rebuffed. Vaughn then tells Will to present his analysis of Kabir to Kendall.

In Kandahar, Kabir observes Sloane admiring a 16th century Buddhist statuette of an ahrat, a destroyer of the enemy. He asks for proof of Sloane's power. Sloane asks him to choose a target.

At the CIA, Will recommends that they contact Aliyah Kazabi, Kabir's ex-wife, who hates him so much that she escaped from his tyranny with their son. She's married to an administrator at the Vatican Embassy in Mexico City. Vaughn and Sydney immediately leave to find her. Sark, meanwhile, has been dispatched to Mexico City, where he hides the Rambaldi weapon in a van outside the embassy. He sets it at 20 percent of its capacity.

Sydney, disguised as an old woman, tracks down Kazabi, who refuses to get involved. Weiss informs Vaughn of a plot to blow up the embassy. He alerts Syd, who knocks Kazabi unconscious to take her with them. As they speed away, those in the embassy and its church burst into flame. Weiss notes a hot spot on his infrared monitor, although Syd and Vaughn see nothing. Upon returning, however, they find dozens of charred bodies. It's enough to sway Kazabi, who decides to help.
A very pleased Kabir, believing his ex-wife to be dead, gives Sloane the ahrat as a gift, as well as $40 million. The CIA traces Sark from Mexico City to Kabul and assumes the operation involved Sloane. Sydney's mission is to enter Kabir's compound and disable the weapon. Marshall explains that the weapon acts like a neutron bomb, emitting high energy, microwave-like pulse. It also knocks out electricity, meaning it can down planes, and there is no defense against it. He shows Sydney a cold suit that she'll wear in order to shield herself from the heat-sensitive cameras at the Helmand base.

Sydney successfully enters Kabir's base but her intel is bad, and she's detected and captured when her mask is knocked off during a fight. Vaughn asks for assistance but Kendall refuses to take the chance. Unless they find another way in, no one will save Sydney. A desperate Vaughn turns to … Dixon.

In Kandahar, Kabir tortures Sydney. As he is about to destroy her knee with a hammer and chisel, he's shot — it's Vaughn and Dixon. They take the device, fight their way out and return home. Syd thanks Dixon, who says that he can't judge her for not telling him about SD-6. At her apartment, Sydney relates to Vaughn that every time they think they have seen the worst, it is far from over.

Sark wonders why Sloane left the weapon with Kabir, who ultimately lost it. Sloane breaks the ahrat, revealing the missing piece of the Rambaldi manuscript page. He places the piece in the missing center, completing the page.