The first season sees the start of the working relationship between Don Eppes, an FBI agent, and his genius brother Charlie, an applied mathematician and professor at a local university.

Charlie successfully predicts the time and place of a bank robbery using what he says are elements of Heisenberg's uncertainty principle, but when the planned arrest goes bad, he retreats into the math problem P vs. NP.

The girl's father (Neil Patrick Harris) is an innovative mathematician, and the kidnapping may be related to his work on the Riemann hypothesis.

Don is assisted by Secret Service agent Kim Hall (Sarah Wayne Callies) while Charlie uses math to analyze fake bank notes and track their spread.

A truck carrying radioactive nuclear waste disappears, and Don figures that a dirty bomb will be set off in downtown Los Angeles.

In 1946 Manhattan Project physicist Louis Slotin used his body to protect fellow scientists during an accident with a plutonium experiment at Los Alamos; he died of exposure to the ionizing radiation 9 days later after his "walking ghost phase".

Final appearance of: Sabrina Lloyd as Terry Lake An unidentified flying object travels over Los Angeles and then disappears.

Don is joined by his former Fugitive Recovery partner Billy Cooper (Max Martini) as the Bureau launches an effort to recapture them.