Don and his team desperately search for Megan, who was kidnapped and taken hostage by a disturbed woman on a violent crime spree.
When a painting worth millions of dollars is stolen from a museum just before it is to go on tour, Don and his team must track down the thief, believing it is part of an insurance scam.
An interpreter in the Chinese consulate is killed in a hit and run, but Charlie figures out that it wasn't an accident and the investigation leads Don to believe there's a leak in the Department of Justice.
A man is shot while driving down the freeway with his two sons. Charlie helps Megan and Don determine if it was a random act or the work of a serial killer.
As the team investigates a murder at a horse-racing track, they discover that there was more than just gambling involved in the murder.
After a series of blackouts, Don and Charlie must investigate and make sure that the blackouts are not acts of terrorism. As the investigation continues, Charlie figures out that the blackouts are all part of an elaborate scheme to break a prison out of jail.
A minor league baseball player dies and the police must determine if the death, caused by steroid usage, was an accident or murder. Charlie uncovers a formula fantasy league players had been using to determine which players were on steroids.
Don, Charlie and the team look into problems with toxic waste disposal when several children are hurt after a sinkhole collapses underneath a school playground.
While investigating the death of a Senator, Don's team discovers that someone is using a behavior modification program, that was discontinued, to get the participants to commit murder. Meanwhile, Larry announces that he is leaving to go to space for six months.
A serial killer starts stalking Internet sexual predators and murdering them to stop them from hurting young girls. The team tracks the killer and discovers that it's the wife of one of the murder victims. Meanwhile, as Larry prepares for his NASA mission, he gets a call telling him he's not going to be able to go after all. Charlie makes a call and vouches for him, and NASA decides to let him go. They family has a send-off party for Larry.
A man finds a teenage girl nearly beaten to death. Don and the team are called in to investigate and discover that the girl escaped from a polygamous cult headed by a leader who is running from the FBI. Charlie and Amita decipher a breeding chart found at the leader's last known location and then track him to his current location. Meanwhile, Alan has dinner with Mildred.
When a marine expert giving a talk to some school children finds a dead body, and a multi-million dollar racing yacht sinks during a race, Don and his team are called in.
When two police officers are murdered during a robbery that is part of a string of robberies at upscale restaurants, Don's team is called in. Charlie helps Don to figure out where the money is being laundered. Meanwhile, Don is required to go see a psychologist and Charlie helps Millie with fundraising for the University.
A badge of a missing LAPD officer is found causing Don and the FBI to re-open the case. The police suspect a former gang member turned activist is responsible, but Charlie analyzes the data and figures out where the police officer was killed leading the FBI to a whole new pool of suspects. Meanwhile, Don and Liz's relationship progresses.
A mixed-martial arts fighter dies training for a championship match. The man who was practicing with him, Ben, turns out to be an old friend of David, so the team is brought into the case.
Don goes to his therapy session and is forced to turn off his cell phone and stay out of contact with his team. Megan must head up the search for a kidnapped boy in Don's absence. Charlie and Amita try to help Megan track down the kidnapper. Meanwhile, Don realizes that he has some control issues.
When an old colleague comes to Charlie with a conspiracy theory and then winds up dead the next day, Charlie calls on Don to investigate. The team connects her death as well as four others to a voter fraud conspiracy. Meanwhile, Megan is asked to take another assignment.
A small plane crashes into the mountains and an officer who is first on the scene is murdered. Charlie hears about the crash and rushes to the scene to figure out what caused the plane to crash. He determines that the plane was carrying undeclared cargo and his calculations lead the FBI to drug smugglers. Meanwhile, there is a break-in at the Epps' home.
Don and Charlie disagree over who is the real serial letter bomber. In the end, they must call on their lead suspect to help them track down the real bomber and disarm one of his bombs. Meanwhile, Millie and Alan make a bet about who can go longer without buying something they don't really need.
Don believes that a death row inmate has an ulterior motive when he suddenly wants to confess the whereabouts of bodies he buried during his days as a hit man for the mob.
Don and the FBI uncover a possible terrorist attack on Los Angeles that targets the city's water supply. Charlie has a difficult time working with a terrorist specialist brought in to work on the case and it turns out that the specialist had something to do with the terrorist attack. Meanwhile, Alan tries to help with the case, but Don doesn't want him working on the cases.
When thieves hijack a truck filled with valuable medical supplies, $50 million dollars intended for a relief effort in Zambia, and two aid workers, the FBI races a second violent crew intent on getting to the goods first. Meanwhile, Don asks Charlie to come to a therapy session with him and they begin repairing their relationship. Don also announces to the team that he is in a relationship with Liz.
After a brilliant bomber tries to give Charlie a message about a "Janus List" of secret service double agents, the team must find the list as well as the bomber's murderer. Megan returns to the team, just in time to learn that their very own agent, Colby, is a spy.