Season 3

When the F.B.I's special assistant Howie claims to have nearly escaped being shot, Jack and the team are skeptical as to the legitimacy of Howie's story. However Howie's tale becomes more and more plausible as other killings arise, all linked to Howie's incident.

Seven Eastern-European terrorists in the D.C area are under suspicion from the F.B.I team who have linked them to an underground organ dealing business. In the meantime, Sue and Lucy struggle to live with Anita, their unannounced, and very picky, house guest.

When a radical environmentalist group blows up an SUV dealership, the team looks into the case with the help of a victim from one of the environmentalist group's earlier fires. Meanwhile, with his cholesterol off the charts, Myles decides to make some changes to his dietary lifestyle.

A special undercover agent from San Diego comes to D.C to assist in an operation involving street drug dealers. But Jack quickly becomes annoyed with the new agent when he starts to show interest in Sue.

A famous actor visits the F.B.I to observe as the team tracks down a gang involved in selling fire arms. Later when the team gets word of a possible terrorist threat, the movie star begins to show interest in Tara.

The team continues their investigation concerning a missing plane which seems to be connected to their terrorist threat. Meanwhile, an unexpected boyfriend of Tara's shows up.

When several 30-year-old women are murdered in a similar fashion, the FBI team suspects a serial killer. At first, their chances of catching the killer seem bleak, but then the murderer makes contact with Sue and leads her through his own game of Simon Says which will lead them all to him.

When the husband of Sue's friend Carol is killed in a boating accident, the team begins to look deeper into the couple's marital history. Meanwhile, Bobby and Myles escort two witnesses on a long and troublesome road trip to Arizona.

Sue and the rest of the team investigate the death of a prominent Senator's son during a college fraternity hazing. But what appears to be an open and shut case of alcohol poisoning takes a surprising turn. Meanwhile, Sue gets a lesson in instant adolescent parenting when Amanda, Sue's twelve-year-old Deaf friend, spends the week.

While Myles battles with a neighbor over a flagpole, a video recording submitted to the FBI is investigated for possible leads.

Continuing their investigation with a newly missing informant, the F.B.I must try and find amnesia-stricken Jonathan as his memory slowly returns, giving him more and more clues that may put an end to the case.

The team investigates the group behind two bombings: one at a restaurant, the other a suicide bomber at a metro station. Meanwhile, Miles embarks on a new vitamin health regime.

When a young woman is kidnapped in broad daylight, Sue and the rest of the team are introduced to Mind Profit - a cult that believes in bringing a person to their true self and has been the link to some mysterious disappearances.

After a small plane crashes in a Virginia field, the team discovers the burned plane contained one million dollars and a small drug stash. In the meantime, Randy enlists Sue's help in preparation for his date with a deaf woman.

After a sophisticated millionaire attempts to rob a bank and is shot down by the police, the F.B.I team investigates further into the businessman's life and find designer drugs at the heart of it. Meanwhile, Sue and Lucy have Levi photographed for dog food advertisements.

Sue and the rest of the team are shocked when Sue's long time informant Troy is arrested for robbing a convenience store. Darcy informs Bobby of a new job offer she's received in California that will force her to move, if she takes it and Myles's recent jaw injury is giving the rest of the team a break while Myles remains silent for five days.

While battling against their very young, inexperienced new supervisor, the team investigates the alleged murder of a senator. However they're not sure whether or not to believe their witness - a schizophrenic who often sees things that are not real.

Sue and the team investigate a bank robbery but this bank robbery becomes a little more interesting than the team expected. They find out that the bank they are investigating was robbed several years earlier. This time they learn that three girls have robbed the bank, which begins to seem strange to the team. When they robbed the bank they stole shoulder pads and one of the girls is the daughter of the president of the bank that was being robbed. Lucy has a mystery of for a long to figure out after her grandmother gives her a jewelry box. When the team opens the box to find out what it contains they are all very surprised at what falls out of the box. Lucy learns that the letters her grandmother kept were from her first love named Oscar. Sue and Lucy decide to track down Oscar because he still wants to see Lucy's grandmother. Lucy is shocked when her grandmother learns of her surprise.

In the series finale Sue Thomas gets promoted to senior investigative analyst for the F.B.I. Sue is thrilled with the promotion but soon realizes that heading to New York City would mean leaving her friends. Jack becomes a victim of identity theft and feel sad when he learns of Sue is promotion. While trying to catch the person who's committing identity theft Jack realizes that he was almost shot at and might never have gotten to say goodbye to Sue.