The city is in a panic as a sniper goes on a shooting spree and randomly kills several people, including a postal worker. The investigation reveals that more than one shooter is at work. As Charlie works the case, he's frustrated by a sniper expert Don brings in to help out.

Don and Agent Weston of the NTSB investigate eyewitness accounts of a mysterious unidentified object flying dangerously close to downtown Los Angeles that has raised concern of a terrorist attack. After Charlie is recruited to help with the investigation, it is discovered that the flying object is part of a new technology that could revolutionize air travel. But the investigation takes a turn when they learn that the lead engineer is found murdered.

Don and his team are called in when a woman attempting to rob a jewelry store in Beverly Hills is shot by a security guard. Charlie assists the FBI by using the keyless remote from the woman's car to help identify her and locate the store owner's kidnapped wife and daughter.

When an assailant opens fire in the FBI offices, Don and his team must determine his motive and possible connection to a dangerous arms dealer who is on trial. After nearly getting shot, Charlie is shaken and reluctant to return to the offices, which hinders his contribution to the case.

The FBI becomes involved when the bodies of young Asian girls are washed up on the beach. The situation becomes more critical when it is discovered one girl has avian flu. As the investigation continues, Don and his team discover a connection between the girls and the sex trade industry. Meanwhile, Amita considers a transfer to Harvard University, which causes Charlie to re-evaluate his feelings for her.

Don and the rest of the team investigate several attacks occurring on LA highways that may be connected.

The problem of the disposal of toxic waste becomes real to Don, Charlie and the team when several children are injured after a sinkhole collapses underneath a school playground. Charlie attempts to help with the case, but faces opposition from his new boss.

Don talks to his therapist again, and while he's gone, the team races to find an eleven year-old boy being held on a $3 million ransom, and time is running out...

Don, Charlie, and the team take on unknown terrorists who may be using nerve gas to undermine Los Angeles' water supply.

Robberies the storybook hero would have been proud to claim plague Don and Charlie as they attempt to catch a do-good thief who is donating his spoils to charity.