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.

Adam Kinsey of ""Final flight"" is assigned to shadow Jack and learn some secrets of the trade and follow the team. Howie tells Sue, Jack, and Adam about some information he got regarding a gun shipment. Otis had plasma screen TV that he wants to sell so he can get out of dealing with the guns. After the team finds the man Otis has been working for Adam requests to see the dead body he learns that looking at a dead body may be harder than he thinks. Adam begins to fall in love with Tara. Things begin to get scary when the team learns that a plane flew into restricted airspace over Washington D.C. and suddenly goes missing after the pilot turns off so the plane can't be spotted.

The Deputy Attorney General has a problem with Jack's handling of the latest case. Jack wants to transport someone who may have possible information on a terrorist attack from Malaysia to the United States. The deputy attorney general denies Jack's request because he fears Jack maybe bringing a terrorist into the United States. Meanwhile Adam Kinsey of "" final flight gets unprecedented access to continue researching his role as an FBI agent. The unprecedented access gives the team problems when his personal gets in the way. Things get slightly more complicated for Tara when Stanley her old boyfriend returns to help crack the code of a possible terrorist plot from "" the king of terror.""

For latest case Sue wants to get into the mind of the serial killer but this case but this case could end her career with the FBI. Things begin to get difficult after Sue get national attention from a newspaper for promising to catch the killer. The first murderer is of a talk-show host whose fingernails were removed and her body was positioned with great care. She was also wearing a scarf. Sue begins doing some research on serial killers minds and how they work. The killer begins chatting with Sue on the Internet and asks her to play a game of "" Simon says "" the serial killer requests that she, alone and play the game, if she doesn't dwell women might die.

Sue runs into an old friend at a deaf and poetry reading. Sue invites Carol to spend time with her and Lucy. Her husband Ted who is a financial money manager keeps Carol from spending time with Sue and Lucy. Leaving Lucy and Sue to wonder if everything is OK between Carol and Ted. Bobby and Myles have the displeasure of escorting Howie and Otis to a case out of town because they are informants in the case. As Bobby and Myles continue on their way to Arizona they learn something about Howie. He won't go to Arizona by plane because of his fear of crashing the plane so that forces Bobby and Myles to drive to Arizona. Tara and Lucy learn that Carol wasn't telling them whole truth. They find out that Ted made a lot of money. They also learn Carol had markings consistent with spousal abuse before, leading Sue, Lucy, Jack, and Tara to believe Carol pushed husband off the boat.

Sue and the team get a highly sensitive case to solve. Senator Fenton requests that the death of his son Kyle be looked into. He tells the team that his son died due to drinking himself to death fraternity initiation. The medical examiner's report on Kyle rules out alcohol poisoning but states that he was allergic peanut oil. Now the team is looking at a homicide and not a simple hazing. Also Sue and Lucy let Amanda stay with them for the night they get an idea of what parenting is like. As the help Amanda deal with going on a date and then being rejected at school. Amanda gets a harsh lesson to learn. She finds out that friends are hard to come by because she is deaf.

Sue and Jack receive a memory stick with some interesting video of to man possibly plotting something. Sue and Jack set out to meet the couple that bought the memory stick to the FBI. When Sue and Jack go the hospital to meet Jonathan they soon have a problem. Johnson is asked to look at a picture of to man and see if he recognizes them, Jonathan unfortunately can only remember his name and nothing else. Jack takes Jonathan to places to see if he can remember anything. Jack takes him to a restaurant and a certain table but the only thing he seems to remember is how to someone to the ground. Jonathan tells Jack that he can't remember where he learned those particular moves. The team takes Jonathan to his hotel room to see if he can remember why he was there. As they begin to search through the mysterious man's belongings they find a suitcase full of money and a gun with a silencer on it and several passports with Johnson's picture on them. They learn that of the fake passports c

We last left the story with Jack and Jessica running into each other in Washington D.C. for the first time. Jessica tells the team that Jonathan wasn't going to be found unless he wanted the team to find him. The team is led to believe that Jonathan killed Mr. Wells and took the hard drive out of his computer. Things only begin to get crazy as Jonathan begins to remember things. Sue gets a message on her blackberry indicating Jonathan would like to talk with her about some things he has remembered. He tells her he remembers seeing a car with license plate. As Sue tries to get more information the team is tracking Jonathan to office building. Jessica gets rather angry when the team loses Jonathan due to his escape from the office building just as he was about to remember something more. Tara begins to discover something interesting about Mr. Wong files that indicates a patriot missile targeting system.

The team tries to figure out why restaurant was blown up by a bomb. As they continue to investigate this discover that Danny is lying to protect his father. They learn that Danny's father works for an organization linked with a terrorist organization.

Sue hears about two women who've died because of a cult called the mind profit. Sue tries to help a young woman named Lily get to know her parents better after they began noticing strange behavior in their daughter. Lilly's parents tried to kidnap Lily said she wouldn't go back to Mind Profit. Sue investigates mind profit and tries to find her self. Sue begins to ask Lily about the dead women. Malcolm Hayden begins to think Sue knows too much and kidnaps her.

Randy makes an odd request of Sue. He asks her for some help with woman he is about to meet there is one problem in the correspondence Randy and his date have shared over the computer she forgot to tell Randy she was deaf. Sue now has to accompany Randy on his date to help him with the sign language.

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.