Sydney, hoping to halt Irina's execution, writes Devlin a letter stating that Jack has deceived the CIA. Later, Vaughn explains to Devlin that he's found Soviet standardised test from the 80s, similar to our own. He believes that Irina stole Jack's research and there may be Soviet sleeper cells here in the U.S. Devlin is doubtful. Vaughn hires Will as a freelancer to look into this issue.

On the plane to Geneva, Jack, who's aware of Sydney's letter, says that Irina's plea was a ploy to get Syd's sympathy. Syd says that her birth is his biggest mistake — it represents his gullibility. They arrive at the hospital incognito — on the operating table, Jack gasses the doctors, then downloads the research as Sydney extracts blood from a dying patient, who says the name Irina. Creating an explosion by mixing ammonia with iodine in a centrifuge, they escape to a helicopter on the roof. Jack explains that Irina had ordered Sark to infect her own operatives and use them as a test group.

Back in L.A., Sloane tells Jack that the mysterious wine was laced with VTX, a compound that counteracts the effects of sodium morphate — meaning Emily is alive or a rival wants the Alliance to think that Emily is alive and that Sloane is a rogue. Later, Sloane enters a church, believing he sees Emily. Jack says he suffering from guilt and says there's a way to put this issue to rest. Later Sloane disinters Emily's remains — her coffin is empty!

Sydney and Vaughn are ordered into quarantine because the strange device they'd seen in Taipei has been found to be the source of the virus. After a worrisome night together awaiting test results, Sydney is found to be negative. Vaughn's tests are less clear but he is later released.

Syd watches on closed circuit TV as Jack tells Senator Douglas during his inquiry that he loves Sydney despite his limitations as a father. Still, Jack will go to jail and Irina will be executed the next day. Sydney commandeers Douglas' limo and forces him to reverse the charges against both Jack and Irina by telling him that a Senator is working for The Alliance and she'll turn her evidence over to the FBI if he doesn't cooperate. It's a lie, but it works.

Meanwhile, at home, Vaughn exhibits bleeding fingernails, the first symptom of the Rambaldi virus.