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Lily Cortez was an Agent working for the Central Intelligence Agency who, whilst stationed over in Afghanistan, had a relationship with Major John Sheppard. This relationship lasted for five months until she was in a Pave Hawk helicopter with Sheppard and Lt. Dixon and the trio discovered a trio of Rangers trying to escape from a Taliban base. Despite being told to return to Bagram Air Base, Sheppard instead decided to save the Rangers against Cortez's protestations, an act which broke off their relationship. (SGA: "Flipside")

Following this act, Sheppard was put on trial for disobeying orders and damaging property belonging to the United States Air Force due to the helicopter being shot and a near crash landing following the rescue. Cortez was able to put a stop to the trial by delivering an affidavit to Judge Vance which stated that Sheppard was to keep his rank and flight privileges, his only punishment being a transfer to McMurdo Air Force Base. This decision was made due to intelligence gathered by the Rangers which Sheppard rescued. (SGA: "Flipside")

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