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The show focuses equally on the relationships among Don Eppes, his brother Charlie Eppes, and their father, Alan Eppes (Judd Hirsch), and on the brothers' efforts to fight crime, usually in Los Angeles. A typical episode begins with a crime, which is subsequently investigated by a team of FBI agents led by Don and mathematically modeled by Charlie, with the help of Larry Fleinhardt (Peter MacNicol) and Amita Ramanujan (Navi Rawat). The insights provided by Charlie's mathematics were always in some way crucial to solving the crime.

Opening: (Voice-over by David Krumholtz) We all use math every day. To predict weather, to tell time, to handle money. Math is more than formulas and equations. It's logic; it's rationality. It's using your mind to solve the biggest mysteries we know.

The first season aired between January 23, 2005, and May 13, 2005, at 10:00 pm on Fridays. It started the working relationship between Los Angeles' FBI field office and Charlie Eppes. The main FBI agents are Charlie's brother, Don Eppes, and Terry Lake, as well as David Sinclair. Don and Charlie's father, Alan Eppes, provides emotional support for the pair, while Professor Larry Fleinhardt and doctoral student Amita Ramanujan provide mathematical support and insights to Charlie. Season one was a half-season, producing only 13 episodes. Sabrina Lloyd played Terry Lake, an agent, in this season; she was later replaced by Diane Farr, who played Megan Reeves.

The second season aired between September 23, 2005, and May 19, 2006, again at 10:00 pm on Fridays. Season two has several changes to Don's FBI team: Terry Lake is reassigned to Washington and two new members join Don and David Sinclair: Megan Reeves and Colby Granger. Charlie is challenged on one of his long-standing mathematical workpieces and starts work on a new theory, cognitive emergence theory. Larry sells his home and assumes a nomadic lifestyle while he becomes romantically involved with Megan. 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 Charlie and his dream of her.

Numb3rs was renewed for a third season,[2] which began airing at 10:00 pm on Friday, September 22, 2006, and ended on May 18, 2007. Charlie and Amita intensify their relationship, as do Larry and Megan, especially after Megan's kidnapping. Amita has trouble adjusting to her new role as a CalSci professor, and Larry announces his leave of absence; he will be on the International Space Station for six months, which greatly distresses Charlie. Charlie and his colleagues are troubled by Dr. Mildred Finch, the newly appointed chair of the CalSci Physics, Mathematics, and Astronomy Division, whom they learn has begun dating Alan.Meanwhile, Don dates Agent Liz Warner and questions his ethics and self worth, and receives counseling. Charlie sees Don's therapist, and the two understand one another more. Despite Don's concerns, Alan engages in some FBI consulting with his engineering knowledge, and Larry returns from the space station, disillusioned. The finale wraps up with a revelation that Colby was a double agent for the Chinese.

Noticeable changes from previous seasons include removing the opening-credit sequence (credits are now done during the first segment of the show), the absence of Peter MacNicol's character for much of the season, and the absence of Diane Farr's character for a few episodes. Peter MacNicol appeared in the first 11 episodes before leaving for the television show 24, but returned to Numbers for the 21st episode of season three ("The Art of Reckoning"). His character's absence was written into the show by becoming a payload specialist on the International Space Station. Diane Farr, pregnant for most of the season, left the show for maternity leave in episode 18 ("Democracy"); her character's absence is explained as a particular assignment to the Department of Justice.

The season premiere aired on September 28, 2007, in the same time slot as in previous seasons, 10:00 pm Eastern Time.[3] Because of the writer's strike, only 12 episodes were initially produced. However, once the strike ended, CBS announced the show's return April 4, 2008, with six episodes.[4] The season ended on May 16, 2008.

As this season starts, Colby Granger escapes from jail and is revealed to be a triple agent. He then rejoins the team. Don and Liz break up halfway through this season after Liz has trouble with Don's trust issues. Amita's parents come to visit, which becomes a secondary theme throughout most of the season. Due to her work at the DOJ, Megan is conflicted by her work and turns to Larry. Near the end of the season, Don's girlfriend from season two, Robin Brooks, returns. Don and Robin then continue their relationship. Charlie attends FBI training camp because he has been working with Don for several years and wants to understand better what his brother does. In the season finale, Megan leaves the team to move back to Washington, DC, and Charlie goes head-to-head with Don about a case. This causes Charlie to send information to scientists in Pakistan. He is subsequently arrested and has his security clearance revoked to 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 more challenging than he expected.

Season five opens three weeks after "When Worlds Collide" (season four's finale), with the government dropping the charges against Charlie. Charlie gets his security clearance back after Don and he fight FBI Security Officer Carl McGowan. Don begins to explore Judaism. The team adds new agent Nikki Betancourt, who arrives shortly after Megan Reeves' departure. Robin is offered a promotion but turns it down. Buck Winters (from the episodes "Spree" and "Two Daughters") breaks out of prison and comes after Don. Alan suddenly finds himself coaching CalSci's basketball team. David becomes Don's primary relief supervisor. DARPA tries to recruit Charlie, but he turns down their offer. 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. Amita is kidnapped, and the team races to find her. After she is rescued, Charlie proposes to Amita. Her response is left undisclosed.

The season starts with the engagement of Charlie and Amita. Soon after, Larry turns down an opportunity to meet with mathematicians at CERN, in Geneva, and drops his course load for the following semester. This leads Charlie to realize Larry is once again leaving and leaving all of his work to Charlie. Don learns that his former mentor is crooked, causing Don angst to shoot his mentor. Charlie and Don realize that Alan has lost a substantial amount of money in his 401(k). After some delay, Larry leaves Los Angeles to find a vacant piece of land for sale within driving distance of the city. Alan decides to return to work and finds a job as a software technical consultant. David asks Don for advice about career paths within the FBI. Larry returns from the desert with a new theory about the universe's fate. Charlie and Amita begin planning their wedding and decide to join the Big Brother/Big Sister program to practice parenting skills. They get married before their move to England to teach at the University of Cambridge. Don loses his gun, recovers it after it is used in some vigilante murders, and gets engaged to Robin. He also decides to leave the team, taking an administrative position within the FBI. Before leaving, Charlie and Amita decide that the family garage should be converted to a guest house so Alan can continue living with them. Leaving Colby, Liz, and Nikki behind, David departs for Washington, DC, to a position as an anti-corruption team leader.

Nicolas Falacci and Cheryl Heuton, the show's creators, have won several awards for the show, including the Carl Sagan Award for Public Understanding of Science in 2006,[32] and the National Science Board's Public Service Award in 2007.[33] They also won the Joint Policy Board for Mathematics (JPBM) reward and encourage communicators who, on a sustained basis, bring mathematical ideas and information to non-mathematical audiences Communications Award in 2010. [34][35]Also, the show's stunt coordinator, Jim Vickers, was nominated for an Emmy Award for Outstanding Stunt Coordination in 2006 for episode 14 of Season 2, "Harvest".[36]

We all use math every day. To predict weather, to tell time, to handle money. Math is more than formulas and equations. It's logic; it's rationality. It's using your mind to solve the biggest mysteries we know.

Several mathematicians work as consultants for each episode.[37][38][39] Actual mathematics are presented in the show; the equations on the chalkboards are mathematically valid, and are somewhat applicable to the situations presented in each show. This mathematical validity and applicability of the equations have been asserted by professional mathematicians.[37][40][41]

Wolfram Research (the developers of Mathematica) is the chief math consultant, reviewing scripts and providing background mathematics for the show. Starting with season four, their website in collaboration with CBS is entitled "The math behind NUMB3RS".[45]

Alice Silverberg, a mathematician consultant to the show, expressed concern with its use of mathematics, asserting that the math is inserted after the initial script and written to provide plausible-sounding jargon, rather than having consultants involved at all stages of story development.[46] The same part-time consultant offered criticism of the show's portrayal of female mathematicians and expressed concern over the appropriateness of the relationship between Charlie Eppes and his graduate student Amita Ramanujan.[46]