Season 2: Episode 9 - "Passage Part 2"
 

At CIA headquarters, Vaughn learns of the PRF ambush on Sydney, Jack and Irina. Sending a rescue team is impossible, since doing so may instigate the Pakistanis. To make matters worse, Vaughn receives a memo stating that the nuclear warheads will be activated the next day at 1700 hours.

The trio makes it to Srinagar and meets Jack's contact. Vaughn contacts Sydney and informs her of the nukes' impending activation. Sydney jokingly tells Vaughn that while some families go miniature golfing, her family hunts for nuclear warheads. Disguised as Pakistanis, they head for the PRF base in an old truck. Jack, under seemingly false pretenses, makes Irina hide in a grain bin stowed in the back. The cars stalls 10 miles from the base and they begin to walk. Irina informs them that the easiest entry into the base is via a sewage tunnel — beyond a minefield that she can navigate. Jack is dubious, but they have no choice.

At SD-6, Sark tells Sloane that he's spoken with the leader of the PRF, Gerard Cuvee, who will upload the "results" to the server after the operation is done. Sloane then receives another mysterious call regarding his wife. A voice demands $100 million in bearer bonds within 24 hours. If Sloane fails to deliver, the voice says, the next delivery will go to the Alliance.

Nearing the PRF facility, Sydney and company are again attacked. Jack this time gives Irina a gun and they repel the attackers. Jack, however, has fallen near a landmine; any movement would set it off. With Irina's guidance, Sydney defuses the device. Meanwhile, Vaughn discovers that the Indians have learned about the nukes and will launch airstrikes in 24 hours against the Pakistani rebels.

Once inside the PRF HQ, Irina determines that the nukes will be in a secure R&D lab, protected by thermal sensors. They must split up, Irina says: she'll deactivate the security system from Cuvee's office, Sydney will raise the lab's temperature so they won't be detected when they enter, and Jack will patch into the voice-recognition system to open the doors. Jack, still skeptical of Irina, reluctantly agrees to the plan.

Sloane meets with The Alliance, informing them that someone has interfered with his wife's assassination and is extorting him. He suggests that they cooperate with the blackmailer and put a tracking device on the bonds. Later, Sloane drops the bonds, which are being tracked by Marshall, at the specified location. To Marshall's dismay, the tracking signal is quickly lost.

Jack and Sydney make it to the lab, only to find that the nukes' plutonium cores are gone. Suddenly, Cuvee enters 3 with Irina alongside! They're incarcerated, and a fearful Sydney watches Cuvee and Irina confront Jack. Cuvee says that years ago he gave Irina the assignment to marry a CIA officer. Irina tells Jack that the PRF has made a deal with Sark. When Cuvee leaves, Irina reveals to Jack that it's just an act, that she was caught and had to play along. She pistol-whips him, but secretly gives him keys to escape.

Irina says that revealing the details earlier might have exposed Sydney as a double agent. The warheads are in Kashmir, she says, at a former maximum security prison that's now the stronghold for the People's Revolutionary Front. Sydney convinces Irina to lead a team to Kashmir. A furious Jack reacts by joining the team himself. He gives Irina a necklace layered with C4, warning her that he would detonate it if she tried to escape.

Vaughn appeals to Indian authorities to delay the airstrikes. He's denied but is given the use of a helicopter to rescue his friends.

Jack frees himself and Sydney, and tells her that Irina said the plutonium cores are being used to activate a Rambaldi artifact — one that, through self-sustaining cell regeneration, proves endless life. They contact Kendall and are told to vacate immediately because of the impending Indian airstrikes. Jack disobeys orders and tires to find Irina.

They make it to the lab, where the PRF is using the cores to activate the artifact. As the airstrikes begin, the artifact opens up — revealing a flower. Jack and Irina, who was in the lab, overpower Cuvee. Vaughn arrives in the helicopter and spirits away Sydney, Jack and Irina.

Back at the CIA, Irina returns to her cell and finds her reward — a fresh set of pillows and blankets. She explains to Syd that she shot her in Taipei to maintain her own cover. Later, Sydney learns from Vaughn that the flowers are 400-600 years old. Vaughn hands her something — tickets to go miniature golfing, which she does with Will and Francie while Vaughn observes from a distance.