Amita has troubles adjusting in her new role as a CalSci professor, and Larry announces his leave of absence—he will be on the space station for six months, which greatly distresses Charlie.

Dr. Mildred Finch, the newly appointed Chair of the CalSci Physics, Mathematics, and Astronomy Division, initially troubles Charlie and his colleagues, as Alan dates her.

Don is on the trail of a criminal couple consisting of a 30-year-old teacher Crystal Hoyle (Kim Dickens) and her 17-year-student Buck Winters (David Gallagher) who are committing crimes across the country.

The team investigates the death of a man armed with a sophisticated statistical analysis that can identify the winning horse at a race track.

A minor league baseball player trying to get back to the majors is found dead of steroid abuse, leading the investigators to an unusual chain of suspects.

A new CalSci administrator (Kathy Najimy in her first appearance as recurring character Dr. Mildred Finch) annoys Charlie and his colleagues, while Alan dates her.

After an extremely expensive yacht sinks in the middle of a race, Charlie finds himself caught between a rock and a hard place when both Don and the NSA need his help on the case.

When two police officers are killed while eating dinner out, Charlie tries to figure out where the killers will strike next while Don's superiors make him see the department shrink (Wendell Pierce) to help him deal with the aftermath of the Crystal Hoyle Case.

Don and the team reopen a cold case when a bunch of kids playing in an abandoned empty construction site discover a police badge.

Don talks to his departmental therapist (Wendell Pierce) again, and while he's gone, the team races against time to find an eleven-year-old boy being held hostage on a $3 million ransom.

Jay Baruchel and Joshua Malina again appear in recurring roles; William Sadler and Kelli O'Hara also guest star.

Don and Charlie hunt for a serial letter bomber and disagree over whether a key suspect, a physics professor (Matt Malloy) working as a consultant on explosives for the Department of Defense who eluded conviction once before, is responsible for the latest murder.

When a former mob hit man on death row suddenly has a change of heart and agrees to confess to his crimes, Don has an uneasy feeling about the whole affair.

A truck loaded with medical relief supplies and $50 million cash is stolen, and someone other than the FBI wants to recover the hijacked shipment.