In Sγo Paulo, Sydney evades Sawaris bodyguard after watching a paramedic team implant a bomb into the pacemaker of UCO speaker Patel. When Sydney awakens in a run-off canal, she contacts Dixon, who grabs a dazed Patel at the UCO conference, and steals an ambulance. As Dixon proceeds to surgically extract the bomb, they are being pursued by Jacqnoud, who controls the detonator to the device. While Sydney drives, Dixon removes the bomb just as Jacqnoud activates it and launches it beneath his car abruptly ending the chase.
In Los Angeles, Francie tells Sydney that they are throwing a big Halloween party at Sydney's apartment. While setting up, Will tells Francie that he's been investigating the death of Danny, whom he has learned was to be on a flight to Hong Kong, not Singapore, and seated next to a woman named Kate Jones - neither of whom made the flight.
Will meets up with the mystery woman, and has clearly done his homework she even admits to having had an affair with Danny. But Will stuns her when he points out that, according to her social security number, Kate Jones died in 1973 and she races away from the meeting place.
Jeroen Schiller works for the Hensel Corporation with information on a vaccine against biological warfare...and Sydney and Dixon's mission is to help Schiller get safe passage into the US. Later, Vaughn introduces Sydney to CIA agent Paul Kelvin, who has been chosen based upon his resemblance to the German. Arriving in Berlin, Sydney uploads the files from Schiller's computer to a remote server, disguised as a network supervisor, before making their escape. Upon removing Schiller from Hensel, agent Kelvin, in further disguise, trades places with Schiller without Dixon's knowledge and doubles as the SD-6 captive, while Schiller returns home with the CIA.
Back at SD-6, Kelvin feeds Sloane a partial computer program that will also run a CIA control into their network, enabling a "back door" for them to see into the SD-6 database. As Sloane questions the CIA operative about the location of a vaccine, which is being perfected into an inhaler form Kelvin realizes he does not know about this...But Sloane is even more suspicious, when he also learns that Sydney had also changed Schiller's drop-off location at the last second.
Knowing that her cover would be blown if Kelvin doesn't learn the location of the inhaler, Sydney asks Jack to assist, after Schiller reveals the location to the CIA. With Sloane viewing on a monitor, Jack quietly feeds Kelvin the location before breaking his arm and passing a convincing message to Sloane about his SD-6 loyalties and Kelvin screams out the location of the plant Badenweiler, Germany.
Sloane sends Sydney and Dixon to Badenweiler to retrieve the inhaler, and then destroy the plant so no one else will have the vaccine. Vaughn informs Sydney that the CIA will rendezvous with her in the building, make a switch with the inhalers and disable the explosive to save the building and its contents. But before departing, Sydney also learns from Vaughn that her father may also be working for the FBI...and she no longer knows where her father's allegiances lie.
In Badenweiler, Sydney disables Dixon's bomb, makes the switch with the CIA agents in the building and gets out. Dixon hits the detonator, and of course, nothing happens. But prepared with a second detonator device, that Sydney knew nothing about, Dixon completes their mission by blowing up the building - with the CIA agents still inside...