Noticeable changes from previous seasons include the removal of the opening credit sequence (credits are now done during the first segment of the show), the absence of Peter Mac Nicol's character for much of the season, and the absence of Diane Farr's character for a few episodes.

Peter Mac Nicol appeared in the first eleven episodes before leaving for the television show 24, but returned to Numbers for the 21st episode of season 3 ("The Art of Reckoning").

For example, in the episode "In Plain Sight" (season 2, episode 8), one of the criminals is named Rolle and Charlie's father mentions a meeting with a man named Robert Peterson. The first season run of the show aired between January 23, 2005, and May 13, 2005, at p.m. It sees the start of the working relationship between Los Angeles' FBI field office and Charlie Eppes.

He is subsequently arrested and has his security clearance revoked, so he can no longer help Don on cases.

At the end of the episode, Don drives away to another case and Charlie admits that giving up FBI work will be harder than he expected.

Amita receives an offer for an assistant professor position at Harvard University, but is plagued by doubt as her relationship with Charlie is challenged and her career is in upheaval.

Alan begins work and dating again, although he struggles with the loss of his wife, and both he and Charlie dream of her. on Friday, September 22, 2006, and ended on May 18, 2007.

Toward the end of the season, Don is stabbed, and Charlie blames himself for it.

The aftermath of Don's stabbing causes Charlie to focus more on his FBI consultation work. Notes about Season Five: "Disturbed" marked the 100th episode of Numbers.

Despite Don's concerns, Alan engages in some FBI consulting with his knowledge of engineering, and Larry returns from the space station, disillusioned.

The finale wraps up with a revelation that Colby was actually a double agent for the Chinese.

Charlie gets his security clearance back after he and Don fight FBI Security Officer Carl Mc Gowan. The team adds new agent Nikki Betancourt, who arrives shortly after Megan Reeves' departure. Buck Winters (from the episodes, "Spree" and "Two Daughters") breaks out of prison and comes after Don.