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.

Jack runs into a bounty hunter named Joe who used to work at the FBI until his daughter died. He blames Jack for his daughter's problems. Although the team searches for Fantasia (a new designer drug) Levi learns that he will grace the box of the latest dog food only to learn that it isn't so easy to do. Sue and Lucy begin the have problems with the photographer that has chosen to photograph Levi. Sue and Lucy learn that Levi will have to compete with the photographer's dog in order to be included in the latest dog calendar.

Sue learns that Troy is being blamed for armed robbery. Sue and Jack set out to prove whether he was part of the armed robbery or not. Darcy has gotten a job in Los Angeles and asks that Bobby go with her to Las Angeles. Bobby and his girlfriend both realize that they've each made the decision regarding Darcy's news. Bobby and Tara begin a relationship with each other. They soon find out that they have lost their love for their respective partners. Troy insists that he didn't do anything in the armed robbery. Sue tells Troy she believes him. Troy insists that he didn't do anything in the armed robbery. Sue tells troy she believes him. After the FBI learns of new video of the armed robbery Sue finds out Troy misled her because he is in the video.

Sue meets a woman who says she saw a murder but the only problem is there are sure whether Beth heard or saw the murder. Sue and Jack find out that their witness is schizophrenic and gives them clues in strange metaphors making the case all the more complicated to figure out. Also the team gets a new acting supervisor named Wayne. Their new supervisor begins to drive them crazy when one begins to color code all their cases. He places the current case as a low priority case. They soon find out that Wayne has never even solved an FBI case in his life.

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.