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Michael C. Vaughn (real name André Michaux), is a secret agent of the CIA and Sydney Bristow's love interest and original handler back during her masquerade as a double agent for SD-6. Vaughn has been with the CIA for many years, following in the footsteps of his father, who incidentally was killed by Sydney's mother, Irina. Vaughn's best friend is Agent Weiss who keeps an eye out for Vaughn's happiness and well-being—to the point of almost getting him killed. After saving the world from a near apocalypse, Vaughn revealed to Sydney that Michael Vaughn was an alias of his shortly before being implicated in an orchestrated car crash.
In the first season, Vaughn serves as Sydney's CIA handler, co-ordinating counter missions in their attempt to take down the terrorist organization, SD-6. Although sexual tension is evident between Vaughn and Sydney throughout this season, the closest these desires come to fruition is when Vaughn rescues Sydney from the FBI by helping prove that she is not the woman who prophecy says will bring about the end of days.
For the second season, Vaughn continues to serve as Syd's handler. That is, until they help bring down the "Alliance of 12" altogether and SD-6 no longer exists. At that point Vaughn just becomes a more generic co-worker of Sydney's. Freed from the bonds of Syd's double agent life, they begin to see each other in a more romantic sense, until Sydney's presumed death. After spending a year thinking that Sydney was dead, Vaughn finally started dating again and married another CIA agent, Lauren Reed. Once Sydney resurfaces, Vaughn becomes very aware of his emotional conflict between his current wife and his ex-girlfriend. After it is revealed that Lauren Reed is a double agent working with Sark, Vaughn confronts Lauren and ultimately kills her.
In season four, Sydney and Vaughn make their relationship known and more pronounced, although they are still noticeable scars. Both agents now work for the secret CIA division called APO ("Authorized Personnel Only") headed by Sloane. United by their distrust for Arvin, the duo manages to run a series of missions together successfully. Eventually, Michael proposes to Sydney right before the Sovogda mission. After a mostly successful mission, Vaughn and Sydney are on their way to Santa Barbara when Vaughn admits to Sydney that Michael Vaughn is simply an alias of sorts he has been using.
In the final season,Vaughn reveals his real name to be André Michaux and that he has been secretly uncovering the identity of Prophet Five for years with one of the CIA's most wanted terrorists, Renée Rienne. During one of their APO missions, Sydney reveals to Vaughn that she is pregnant with their baby. However, after Vaughn is shot several times by Gordon Dean and presumably dies, Sydney teams up with Renée to try to uncover the truth about Prophet Five, despite being several months pregnant. When Sydney gives birth, Jack sends out a message to Bhutan and it is revealed that they faked Vaughn's death in order to hide his existence from Prophet Five.