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The Counteragent is the seventh episode of the second season of Alias, and the twenty-ninth episode overall.
Starring: Jennifer Garner (Sydney Bristow), Ron Rifkin (Arvin Sloane), Michael Vartan (Michael Vaughn), Bradley Cooper (Will Tippin), Merrin Dungey (Francie Calfo), Carl Lumbly (Marcus Dixon), (credit only) Kevin Weisman (Marshall Flinkman), David Anders (Julian Sark)
Guest Starring: Austin Tichenor (Dr. Nicholas), Petra Wright (Alice), Chris Ellis (CIA Agent Chapman), Victor McCay (CIA Agent Rudman), Stephen Davies (Sark Associate), Stephen Mendillo (Henry Fields)
Vaughn alerts CIA Dr. Nicholas that he is showing the first sign of exposure. Not heeding his advice to wait for a medical team, Vaughn visits Irina Derevko first. Asking for help about regarding the virus, Derevko agrees to help in exchange for details about his relationship with Sydney. Vaughn collapses soon after the meeting and the doctor's best estimate is that he has approximately three days before the virus kills him.
Irina tells the CIA that there is an antidote located at a defunct Soviet nuclear submarine training base in Paldiski, Estonia currently being run by Sark. The viral antidote is such that a sample of the person's blood must be taken to the facility so that a custom antidote can be manufactured, meaning Sydney must take Vaughn's blood into the facility and operate one of the automated decontamination units.
Arriving underwater and disabling guards with a tranquilizing gun, Sydney is able to move around freely by wearing a large contamination suit and spots Sark observing operations at the facility. Moving to one of the antidote stations, she provides the CIA with remote access to break the security code. They notice that even with the proper code, the activation of the machine will notify central security. Despite orders to abort the mission, Sydney goes forward. An alarm goes off shortly after she synthesizes the antidote and Sydney finds herself trapped in an industrial decontamination room. Sark appears in an overhead observation room behind bulletproof glass and begins to douse her suit with ammonia flurochloride. Informing her that the suit will corrode in a matter of seconds, he gives her an ultimatum to leave her alive and get the custom antidote if she will give him Sloane so that he can kill him. To this, Sydney agrees, although she won't receive the antidote until Sark has Sloane, giving them little time.
Her father helps her in the operation to capture Sloane. Jack distracts Marshall long enough to get Sloane's itinerary for a trip to meet with the Alliance of Twelve. Sloane will be staying at a Yakuze run hotel in Japan and their plan is to capture him before the meeting. Sydney, dressed as a geisha with full face makeup, relieves Sloane's masseuse and stabs him with a concealed needle. Sark's men take the unconscious Sloane by posing as ambulance workers and Jack is given the antidote by one of Sark's men. Sark, as is his usual style, comments on how successful Sydney is and notes how good it is to be working with her.
With the antidote, Vaughn makes a quick recovery and fulfills his obligation by telling Irina how knowing Sydney has made his life both great and difficult. Irina notes that the person Vaughn should really be telling this is Sydney, inspiring Vaughn to try and catch Sydney before she leaves the CIA building although he isn't able to catch her. Back at SD-6, Sydney is surprised to find Sloane back at his office. More surprisingly Sloane is in his office with Sark, who has willingly decided to join forces with Sloane. Sloane tasks Sydney with the debriefing of Sark and while alone, Sark tells her that after waking Sloane he enlisted his help with two offers of good faith. Sark had told Sloane that there was an assassination attempt on his life and had abducted him to prevent his death. He also provided Sloane with a piece of paper with some form of valuable information on it, although he doesn't tell Sydney the nature of the information. Sloane presents Sark to the Alliance, who bring him on as a new ally and goes well to cementing Sloane's reputation with the Alliance.
- Sydney beats two of Sark's guards to get his gun and beats a Yakuza guard in hand to hand combat.
- Sydney uses underwater propulsion thrusters giving her a speed of 5 knots and uses an H&K P-11 Underwater Pistol, capable of firing five tranquilizing darts.
- Sydney goes undercover as a Yakuza masseuse.
- Alison Krauss - "Slumber My Darling"
- Peter Gabriel - "I Grieve"
- Sheryl Crow - "I Shall Believe"
- Debbie Weisberg - "Home"
- Civil Twilight - "Human"
- Amy Stroup - "With Wings"
- The research Will has done on the Project Christmas finds that the archived test was a faked replacement. When casually talking about it with Francie, she notes a test question about the 1983 American invasion of Greneda in a 1982 test. Contacting the official test creator, he notes that the test is not the one he had written and that it was likely administered to over 5 million children in 1982. It is also suggested that Irina Derevko's primary purpose may have been to steal Project Christmas from Jack for the KGB.
- The virus, identified as coming from the suspended red solution in the Rambaldi machine, causes an "ascending paralysis" that starts at the feet and eventually causes death by preventing respiration.
- In a deal for the antidote, Sydney makes a deal with Sark to give him Sloane to kill. She is later surprised to find that Sark didn't kill Sloane, but instead has now joined forces.
- Thanks to Sydney's efforts, she is able to procure an antidote for the virus and it's administered to Vaughn in time.