Charlie's life is put in danger after he gives an interview about the case he and Don are working on together, attracting the attention of the kidnappers of an investigative reporter.
A meth lab bust yields a surprise arrest that stymies the team when they can't figure out why he was in the area, and Megan disagrees with what Don chooses to do to get his answers.
A.U.S.A. Robin Brooks is back in town, and her involvement in Don's case brings back memories as they try to keep witnesses alive. Meanwhile, David attempts to bond with a young man who's in the chief suspect's thrall.
Clay Porter returns to the U.S. when his father and sister are taken hostage, and Don embarks on a deadly cat-and-mouse game to try to catch Porter and rescue his family.
The murder of a rapper puts Charlie to work analyzing the mathematics of the music business in the same week that Amita's parents come to town, and Megan has asked for a week off without discussing it with Don.
When one of Charlie's friends, a scientist at the university, is arrested for terrorist activities, it puts him at philosophical odds with Don. And as he works to prove the man's innocence, his beliefs may jeopardize his career.
The team races to find a group of kidnappers who have their victims drain their bank accounts using ATMs, and Charlie's attempt to reinstate his clearance is slowed by an agent with an agenda that may include Don.
Charlie and Don's fates hang in the balance as the team tracks a white-collar criminal through Los Angeles. Meanwhile, Alan finds out that one of his old planning projects may disappear with a new development by the city.
The death of an agent kicks everyone into high gear, but that slows down when their prime suspect turns out to have Autism Spectrum Disorder, Charlie steps on toes re-establishing himself as the resident expert, and Don looks for deeper meaning.
Two trains collide, a passenger train and a freight train carrying toxic chemicals. Don, Charlie and the team are brought to the scene, investigating a potential crime.
The team descends into a bit of madness as working with a conspiracy theorist to solve bombing case exposes each of their own peculiar beliefs. Meanwhile, a mysterious stranger saves an agent's life.