A toxic gas is released on a Los Angeles subway during an antiterrorism drill run by the Department of Homeland Security. Don must determine whether it was an accident or a legitimate attack before more drills are carried out over the next few days in various locations across the U.S. Back at home, old wounds are reopened between Don and Charlie when they learn that a girl they fought over in high school is going to use their dad's house for her wedding.

Don investigates a series of home invasions in which the thieves steal only high-end items from wealthy individuals. In the latest robbery, a father is killed trying to protect his family. Meanwhile, Charlie becomes upset when a rival theoretician challenges his most famous work and states that it is flawed. Back at home, Alan prepares to open his own consulting business.

Megan feels responsible for an agent's death following an explosion at a house where methamphetamine is being illegally produced that the FBI targeted for a bust. While several men are arrested in the raid, the kingpin gets away and it's discovered that he may also be involved in child pornography. When Charlie learns this and sees a disturbing picture of a young girl at the raid site, he becomes obsessed with finding her.

Don learns that someone is poisoning non-prescription drugs made by a leading pharmaceutical company after four people nearly die from the tampering. The perpetrator then publishes a manifesto in a local paper that leads Don to believe that the person may be a former employee of the drug company. Later, Larry shares his theory of the case with Megan and he discovers that he's attracted to her.

A woman researcher who specializes in Native American antiquities is attacked and killed at the museum where she works. The museum is located on federal land, so the FBI is called in. Don's investigation reveals that the woman was working late at night on a secret project that involved the carbon dating of an object. Back at home, Don and Charlie become worried about their dad after they learn that he is still holding on to his late wife's clothes, which he supposedly gave away months ago.

An arsonist believed to be part of an extremist environmental group sets a fire at a car dealership that kills a salesman. The group's name is spray painted at the scene. It's the fourth such fire, but the first to claim a life. The activist group denies setting the blazes, which leaves Don with the task of determining whether it or someone else is responsible. Charlie tries to figure out if there is a pattern to the fires that would help provide a profile of the arsonist.

An FBI agent working undercover as a gang member is gunned down in a parking lot by a drive-by shooter. Don and Charlie try to determine whether the agent's cover was blown or if he was killed for another reason. Their investigation reveals that the shooting may be linked to other murders in the area. Back at home, Alan prepares to go out on a date and he asks his sons for advice.

A Russian student at a local college is robbed and shot to death in the parking garage of a gambling club after winning big at blackjack. In the victim's car, Don discovers a notebook containing card-counting calculations. The investigation reveals that the dead man was part of a team that cheated at cards and that his teammates may be in danger. Later, Larry admits that he was once addicted to gambling.

A southeast Asian teen is found in the blood-spattered basement of an old downtown hotel, where she was apparently being tortured. But the investigation soon reveals that the girl, along with three other missing women, are victims of a black-market organ-harvesting scheme. Don and Charlie try to find the remaining women before their organs are taken. Amita also helps out by communicating with the teen, who is from the same area of India where Amita's family once lived.

A DNA synthesizer that has the capability of customizing diseases is stolen from the campus where Charlie teaches. Don fears the thieves may be terrorists out to start or advance a bio-warfare program. He also believes the theft was an inside job and the chief suspect is one of Larry's top students. Back at home, Charlie discovers that his late mother was once a gifted musician.

A pedestrian is killed when a homemade bomb explodes under a car outside of a downtown Army recruiting center. The investigation reveals that a similar bombing occurred exactly 35 years ago at an ROTC office that killed two people. The bomber was identified but never captured. A retired agent who worked the first crime is brought in to help with the new case, and Don must determine whether the original bomber has resurfaced or if a copycat is responsible.

The bodies of three illegal-immigrant women are found on government-owned land in a wilderness area. Don investigates and learns that a psychic led the police to the crime scene after allegedly seeing visions of the bodies. The probe also reveals that the women were cut open and that religious artifacts were spread around their remains. When Charlie learns that a psychic is helping with the case, he is outraged and sets out to prove the man is a fraud.

An Iraqi woman visiting the U.S. to participate in a documentary about women's rights in Muslim countries is murdered outside of her cousin's apartment building. The investigation reveals that the killer wore U.S. Army boots and committed the crime with an Army knife. Also, Charlie's former girlfriend arrives from London on a book tour, and their relationship heats up faster than either one of them anticipated.

Two gunmen kill 7 students and a teacher, and wound 12 other people during a shooting spree at a high school. One of the gunmen is a fellow student who is gunned down during the attack. During the investigation, Charlie uses a tracking system to pinpoint the shooters' movements and concludes that a third shooter may have been involved. Also, Larry asks Megan out to dinner, but their time is spent mostly talking about the shootings.

A female federal agent who was once romantically involved with Don apparently commits suicide, but Don suspects she may have been murdered. Charlie joins the case and tries to determine the likelihood of the woman killing herself. The probe reveals that the victim was suffering from depression and that her marriage was in trouble. She had also been investigating a series of armed robberies that could possibly be linked to her death.

A real-estate broker disarms an agent and goes on a shooting spree through FBI headquarters. During the rampage, two agents are wounded and a convicted sex offender, who was being questioned in the beating of a teenage girl, is killed. Also, Charlie is nearly hit with a bullet and later has difficulty shaking the experience. The investigation reveals that more than one person may be involved and that another shooting may be planned.

Don's checking and savings accounts are wiped out by computer hackers after he nabs part of a team involved in credit-card scams. The two arrested men claim they were forced to work for some Russian men who may be connected to the mob. It quickly becomes clear that the mobsters are after Don, which makes him fearful that Charlie and his dad may also become targets.

The bodies of four Asian women wash up on shore following a storm, and a fifth woman is found alive floating in the water. An autopsy reveals that one of the victims has the bird-flu strain in her body, and Don worries there could be a pandemic if she came in contact with anyone else. Meanwhile, Charlie studies ocean currents in an attempt to determine where the girls may have fallen into the water, while Amita gives Charlie some surprising news.

Don investigates the murders of two young women found slumped over in their cars outside of their respective homes. The deaths were made to look like drug overdoses, but Don realizes that a serial killer is at work. Meanwhile, Charlie has bizarre dreams about his parents. In one of them, Charlie's deceased mother appears and tells him that he has a question to ask her, but he can't think what it could possibly be.