At the CIA, Sydney, having learned that Vaughn is sick, asks Irina if there is an antidote. It's in Paldiski, Estonia, she says, at a former Soviet training base for nuclear submarine personnel. But the antidote is genetic-specific, meaning Sydney must manufacture it from Vaughn's blood. With Vaughn now in the hospital and expected to live only three days, Sydney draws his blood and they hold hands. On her way out, Sydney meets Alice, Vaughn's girlfriend.

Sloane confesses to Jack that he's insecure about his standing within the Alliance and that he confessed the Emily issue to Kristof, whom he must now meet in Tokyo. He tortures Richter, desperately trying to find the location of Derevko's ops base.

Will gets hold of the '82 standardised test and finds that it contains no spatial relations questions. Later, Francie recognises that the test is actually from '83 because it references the American invasion of Grenada. Will then speaks to an official at the Dept. of Education who gives him the actual '82 test, which has spatial relations questions. The official is baffled — he had submitted the test without such questions.

Sydney arrives at the Paldiski lab and dons a hazmat suit. She spots Sark. Finding the equipment, she learns that an alarm will sound if she tries to generate the serum. She ignores Kendall's order to abort and makes the serum, thus alerting Sark to her presence. Sark traps her in a decontamination chamber and threatens to kill her by releasing ammonia flurochloride. He forces her to cuts a deal — Sydney can keep the antidote if she'll deliver him Sloane.

At the CIA, Jack supports her plan, mentioning that Sloane will be in Tokyo. As Sydney prepares for the mission, Jack says he never wanted her to be involved in pre-meditated murder, and hints that it's Irina's influence on her. In a Tokyo hotel, Sydney, dressed as a geisha, overtakes a pair of guards and replaces a masseuse administering to Sloane. Syd stabs him with poisoned prongs from her hairpin and he passes out. Sark spirits away Sloane in an ambulance. A Sark associate gives the antidote to Jack.

In LA, Vaughn awakes from a 40-hour sleep. Jack tells him the antidote has been administered and Sloane is dead as a consequence.

At SD-6, Sydney surprisingly sees Sloane — with Sark! He says Sark is cooperating with SD-6 on the search for Derevko. In private, Sark explains to Syd that he revived Sloane and convinced him that they should work together to solve the Rambaldi mystery. Sark then diminished Sloane's doubts by giving him a mysterious piece of paper.

A healthy Vaughn returns to Irina's cell. He confesses his feelings for Sydney. Irina says he hasn't said anything to the one that matters. He leaves her and runs into Syd, who hugs him and cries. She says that Sloane increased his standing in the Alliance by presenting Sark as their new ally. Vaughn says he knows that Syd met Alice, but Sydney tells him not to explain and leaves. Vaughn hesitates a moment and follows, but she's gone.