When Gibbs returned, Lee ceased to be on the MCRT, but she continued to work for NCIS in the legal department.
Special Agent Michelle Lee was the newest addition to the NCIS Team based out of Washington Naval Yard. She was brought in between Seasons Three and Four to bring the team back up to full strength following Supervisory Special Agent Leroy Jethro Gibbs's departure in the aftermath of the Cape Fear bombing disaster.
As the newest member of the team, Lee was referred to as "probie," replacing Timothy McGee in that designation since McGee had moved up in position.
Following Gibbs's return early in Season Four, Lee was transferred to the legal department and was frequently seen delivering warrants to the team.
Lee was also a Harvard Law School graduate. Subsequent episodes also revealed her to be involved in a secret relationship with Medical Assistant James Palmer. When series creator Donald Bellisario was asked by Australian magazine TV Week where their relationship was going, he said it wasn't a relationship, just sex.
At the end of Season Five, Lee, along with Agents Brent Langer and Daniel Keating, was transferred to Gibbs' team. It was later revealed that the reason for the transfer was that there was a mole in NCIS revealing US military information; Lee, Langer, and Keating were the suspects; and the trio were placed on Gibbs' team in order to bring them under closer scrutiny and help determine which one of them was the mole.
In the season 6 premiere episode, Last Man Standing (episode), it was revealed (to the audience) that Lee was the mole in NCIS. In a confrontation unseen by anyone else, Lee shot and killed Agent Langer, and immediately afterward claimed self-defense and accused Langer of being the mole. Lee was temporarily cleared as a suspect, but in Collateral Damage (episode), Gibbs began to suspect that Lee, not Langer, was the mole.
With the approval of Director Leon Vance, Gibbs developed a plan to expose and trap Agent Lee. The plan, implemented in the episode, Cloak (episode) was successful, and Agent Lee was captured in the act of espionage. Under questioning by Gibbs, Lee confessed to being the mole and revealed that she had been acting under duress: Her daughter Amanda Lee was being held hostage and used as leverage to force Lee to provide information.
Agent Lee's capture and confession were suppressed in order to conduct an investigation in the next episode, Dagger (episode) to determine the veracity of her statements. The investigation revealed that Amanda was not Lee's daughter, but her adopted sister, whom she had raised like a daughter. Amanda was rescued by Anthony DiNozzo and Ziva David while Gibbs and Lee exposed a terrorist named Ted Bankston attempting to acquire the information Lee had been passing on.
When Agent Lee learned Amanda was safe, she realized that her mission had been accomplished, and allowed herself to be sacrificed in order to end Bankston. Gibbs had his gun drawn and aimed at Bankston, but didn't have a clear shot because Bankston was using Lee as a human shield.
Lee looked Gibbs in the eye and silently nodded, giving him permission to fire which Gibbs did, killing both Lee and Bankston in the process. At the conclusion of the episode, Gibbs gave Agent Lee's NCIS badge to Amanda.
NCIS Director Leon Vance later remarked to Gibbs that death had probably been a good thing for Lee because if she had survived, then it's most likely she would have spent the rest of her life in prison given the charges of treason against her.