Agent Granger finds himself in prison after it is uncovered that he is a mole for the Chinese in the FBI. But when Granger escapes, Don and his team must track him down and uncover the tangled truth behind it all. Charlie considers trying to have his paper on the mathematics of friendship published.

Secrets and blackmail are revealed when a woman is murdered in an up and coming actor's home in the Hollywood Hills. Charlie and Amita discover that DVD piracy is linked into the blackmail scheme.

A typical morning at a coffee shop is thrown into chaos when a car slams into the cafe, killing one and injuring several. However, the team soon finds that it may not be an accident after all. Larry suggests that Dr. Ray Galuski, a mechanical engineering professor, might be very helpful in the investigation. Ray and Alan hit it off immediately and soon Alan is going back to school part time.

After breaking the patterns in Bible verses that a killer leaves behind, Don and his team are able to track the killer, but remain one step behind. The investigation is complicated by an interested individual following the case who is stalking the team as they proceed.

A private safe deposit bank that holds millions of dollars for the rich and famous is robbed, but the contents of safety deposit boxes are later donated to charities. The items have been stolen from less than upstanding individuals. Don and Charlie must find out who is behind the Robin Hood chain of events. Charlie and Amita disagree over an initial meeting with Amita's parents. Dr. Fleinhardt and Alan engage in a CalSci campus tradition of dropping pumpkins frozen in liquid nitrogen from the top of buildings.

When a member of the Witness Security Program is murdered in cold blood in her home, Don can't help but feel responsible for her death. As the investigation unfolds, a twisted trail leads to organized crime in Albuquerque, a Los Angeles street gang, and a drug dealer from Seattle. Meanwhile, Charlie's book, The Attraction Equation, is published and he attends his first book signing.

Don and his team enter the world of alternate-reality games following the death of a man who was participating in a game. The victim was an Assistant US Attorney, thus putting it within FBI jurisdiction. During the investigation, Amita's life is threatened when her hidden ability helps to find the killer. Meanwhile, Charlie makes a television appearence to promote his new book, The Attraction Equation. Charlie and Amita discuss the possibility of living together. Dr. Larry Fleinhardt returns to campus from his sabbatical following his outer space adventure.

A high-profile heiress is kidnapped by a group who is out to attack her father. Don and the team try to save her, but their rescue mission takes a shocking turn when they learn the group's true motive. The circumstances of the investigation hit a bit close to home for Megan, causing Don to reign her in. Don and Liz attempt to determine where their relationship is heading. Larry and Megan rekindle their relationship.

Charlie helps Don and his team find a rare vintage ashcan version of a comic book that was stolen from a comic book mogul at a convention. The investigation becomes more complex when 14 forgeries of the comic book suddenly appear in the wake of the theft. Meanwhile, Charlie finds himself the subject of a profile piece in Vanity Fair magazine due to the popularity of his book. He becomes concerned that the article is going to slam him because he has very few close personal relationships outside of family and work.

A former FBI subcontractor guns down an agent inside the agency's headquarters and takes a member of Don's team hostage. Charlie and Alan, who are visiting the FBI office, assist in resolving the situation. Megan and Liz take to the field to learn more about the hostage taker.

Someone is trying to physically intimidate Charlie so he will stop working a case where an investigative journalist has gone missing. Meanwhile, Professor Ray Galuski has been helping Alan do some projects around the Eppes homestead. When Ray suggests a number of improvements to make the home more environmentally friendly Alan gets upset at the thought of changing things.

A police officer who is also a serial rapist, uses his position to lure victims. The rapist is being sought by Don and his team. Don and Megan experience difficulties with a female Internal Affairs Officer from the LAPD who jeopardizes the investigation by jumping to conclusions and browbeating witnesses. Meanwhile, it's a full house for the weekend at the Eppes family home as Alan has invited Dr. Larry Fleinhardt for the weekend without knowing that Charlie has invited Amita to spend the weekend because her residence is being fumigated. Larry asks Amita to join him on an important project and is relieved when Charlie enthusiastically supports the idea.

Don and the team bust a meth lab, but Don's instinct leads him to arrest a bystander who is planning an even greater scheme.

Don's former girlfriend, Robin Brooks, returns to California to prosecute a criminal. However, when the witnesses for the case are murdered, Don and the team worry that the next victim will be Robin.

Don and his team hunt for an ex-Marine wanted for murder. Things become confusing, however, when the Marine's family is kidnapped. Is there more to this case than meets the eye?

An FBI team investigates a mass poisoning at a cult compound in which the survivors refuse any medical assistance. What is uncovered is a history of bad blood between members and a murder conspiracy.

A drive by shooting takes the life of a rap star and a further investigation shows evidence of a possible conspiracy , including embezzlement and bribery. Meanwhile, Charlie prepares to meet Amita's parents.

Differing beliefs leaves Charlie and Don in a conflict when they investigate a case involving national security. Meanwhile, Megan decides to leave the team after a crisis of conscience.