When FBI agent Don Eppes finds several murders are linked to counterfeiting, his mathematically genial brother Charlie uses his skills to do what other investigating methods -as used by Agent Kim Hall, Don's colleague and ex in his Albuquerque days, a blank chapter in his past for Charlie- failed to, locate the forging and identify who did the graphical artwork required for his old-fashioned, relatively hard to detect fakes with real printing presses and watermark, not computer printing: it's a missing artist, who must be kidnapped and will probably by murdered as a liability for the counterfeiters...
When Riley, who practiced an ingenious pyramid method of skinning numerous bank accounts for over half a million dollars, is strangled, exactly the same way -not revealed to the press- as Lisa Bayle, for whose murder Don Eppes' investigation once put Cliff Howard in jail after a plea bargain-confession, Don now fears the wrong man was arrested. Charlie helps him quantify the unlikeliness of a coincidence and seriously doubt the forensic evidence. Electrician Jose Salazar, whom Don suspects, still turns out to be innocent of Lisa's murder, but Charlie realizes that's not the point: what if a third person committed both murders, linked rather by the victims?
A truck of nuclear materials is stolen by terrorists who intend to use the materials to make a bomb which would then be used on the city of LA. Only Charlie and Charlie's father Alan can save the city from a small nuclear blast.
Dr. Larry Fleinhardt's former college days friend Jonas Hoke, the Senior computer-science researcher, who develops for Robert Oliver's firm Lorman group with gifted college drop-out Scott Reynolds a classified program to evaluate government projects, is murdered in his Hollywood Hills home; data were stolen from his computer, which only contains a coded program for analysis of baseball statistics. Hoke's financial divorce complications seem irrelevant, although his wife had a relationship with their security system installer Lucas Grant. However Charlie finds that Hoke actually used the same kind of advanced statistic analysis and performance prediction on other data, cleverly masked under meaningless baseball numbers: Hoke applied this method cutting-edge to calculate human performance prospects in real life, based on various governmental and other data, potentially far more valuable...
A UFO is briefly seen flying through Los Angeles with no clear indication on what it is, but Agent Eppes discovers it was heading for the Staples Center and starts an investigation into the possibility of mass terrorism.
A prison transport bus crashes after maneuvers by two other vehicles, several inmates escape, including the dangerous McDowd. Charlie gets on well with CHP Officer Morris on the scene and works out mathematically it was no accident, both other drivers probably were in the game. Dad is worried Don might be returning to the period he regularly worked in fugitive retrieval, especially now a former colleague, burly federal marshal Cooper, is on the same case. After finding a lesser fugitive, Charlie's mathematical probabilities approach helps reconstructing the remarkable movements of McDowd in LA, which leads to a worrisome motive relating to a DEA case and likely further accomplices...
Singer Skyler Wyatt reports a knife-wielding intruder in her home. The break-in seems to be connected to the hate mail she has been receiving for the last three months. Don begins to investigate and the body of a paparazzo is discovered overlooking Skyler's home. Don brings in his brother Charlie to analyze the hand-written hate mail and to try to determine where the strange photographs found on the dead body were taken. As the investigation proceeds the brothers are drawn further into the murky world of the paparazzi and celebrity stalking!
The raid on a small time forgers home reveals a secret code book. Don takes the code book to his brother Charlie who tells him that the book hides secrets of a skilled and highly trained assassin somewhere in the country. Interrogation of he forger reveals the name of the intended target, Gabriel Ruiz, the last remaining member of a powerful political family in Colombia. So the hunt begins to catch the assassin before he completes his mission!
When a death results from an anti-terrorism exercise Don and his team are called in, but they end up butting heads with the leader of the unit who refuses to halt further training exercises. Back at home, Alan has volunteered the house for the wedding of a girl both Charlie and Don had a crush on in high school.
Data from a meth lab explosion reveals a photograph that triggers memories for Charlie and put him at loggerheads with Don who's focused on tracking down the drug dealer who set off the explosion that killed one of his agents.
A psychic helps to find a burial site of numerous illegal immigrants just across the California-Mexico border. Charlie and he battle to see who will come up with the location of another female migrant before she joins the other victims in the morgue.
After an Iraqi woman - in the US to film an interview on atrocities against women back home - is murdered, clues lead to an American military suspect and the team must determine their truth before another killing occurs.
Don and the team investigate a suspicious death at a horse track. When Charlie starts looking into the crime, he uncovers something that will send the investigation into an entirely different direction.
Multiple robberies at upscale restaurants bring Don's team in once it escalates to murder. Elsewhere, both Charlie and Don must do some soul searching as one tackles a psychiatric review and another questions the ethics of a pharmaceutical company that wants to use his name.
The discovery of a presumed dead police officer's badge brings the LAPD and Don's team together to solve the mystery of what happened 17 years ago. Elsewhere, Alan is served in a lawsuit, and he has to determine if his calculations were wrong when he consulted for a golf course.
One of David's childhood friends is accused of murder while sparring in preparation for an All-Out Fighting bout, and Charlie has a contest of his own trying to defend Larry's chair in a Texas Hold 'em qualifier.
An old colleague of Charlie's asks for help because of the untimely deaths of some coworkers, but when she also turns up dead Don and Charlie are started on a trail that may threaten the very democracy they've vowed to protect.
A shipment of medicine and cash bound for Zambia is hijacked, and Don and his team find themselves working against a banker focused on retrieving his money at the cost of the people being held for the code to access the safe.
Peter MacNicol returns as a regular cast member. Colby is being interrogated by a man named Agent Kirkland, who passes him a handcuff key and gives him escape instructions. Don and his team get information about and from Colby and must figure out if that information is reliable then realizes that everything about Colby being a double agent may not be what it seems.
In this episode, it is discovered that someone has stolen, recreated and sold several copies of an extremely rare comic book. Christopher Lloyd plays the original creator of the comic book, who no longer benefits from his past creations. Having thought that his comics wouldn't be worth much in the future, he either lost or sold his entire collection and regrets it now that he and his wife live on very little. His young friend and fellow comics artist, played by Ben Feldman, publicly humiliates the rich man who owned the original before it was stolen.
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.
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.
The abduction of an undercover agent brings ex-CIA psychic Simon Kraft back into the Eppes' lives, and while Charlie pursues a scientific solution and Don a procedural one, Kraft's visions lead them toward an ancient ceremony and the loss of another life.
When Robin Brooks loses a case involving the murder of an informant, the team takes it very personally. Launching an investigation to get around double jeopardy, and bring justice down on an international arms dealer.
An old friend who's a DEA agent agrees to assist Liz in an undercover operation when Charlie uses math to affect the city's drug traffic, but a miscalculation and an addiction endangers both her life and the operation.
Charlie is distracted from applying math to his first basketball-coaching job when a doctor claims to have evidence that clears a death-row inmate, leaving him and the team very little time to be sure real justice occurs.
Charlie takes a very personal interest when one of CalSci's professors is murdered during a raid by animal rights advocates, and once the murderer is found Nikki's actions put the operation and civilians at risk.
A rash of apparent suicides takes a sinister turn when a gambling connection is uncovered. Elsewhere, Charlie worries when Alan's retirement disappears, and Larry flounders trying to find his new path.
The team gets a close-up look at the movie business when a producer's desiccated body is found in the desert. Elsewhere, Larry knows that he's leaving but not his destination, and Alan struggles with technology.
The team explores an odd death by some kind of electricity at a decommissioned airbase, finding themselves teamed with an odd character from the Pentagon's Department 44. Elsewhere, David ponders his future and Alan celebrates a birthday.
The team gets into a turf war with a prison warden, and the casualty may be Ian Edgerton and the member of Don's team that he's taken hostage in a desperate attempt to prove himself innocent of murder charges.
When robbers hit a diamond exchange and take hostages, Don and the team find an unlikely ally in convict John Buckley, who may help the team's investigation when they believe the men are copying Buckley's criminal strategies.
When the team foils a robbery of an armored car full of Federal Reserve money and recover bills that trace back to the infamous D.B. Cooper heist, they call on Agent Roger Bloom, who worked on the Cooper case, for help with the investigation.
Don and the team try their luck at investigating the theft of scratch-off lottery tickets, but the stakes are raised when one of the culprits killed at a botched robbery turns out to be a former lottery winner.
The team searches for a lost shipment of high-caliber firearms when one of the weapons is responsible for random killings throughout the city. Also, Charlie and Amita disagree on a wedding date while Don re-evaluates his relationship with Robin.
The team investigates the deaths of two men who were part of a group of friends that had been sexually assaulted by a teacher when they were young boys. Also, Charlie and Amita get a fantastic job opportunity that could put a wrinkle in their wedding plans.
Charlie and Amita are getting married at last. While making an arrest, Don's gun is stolen from him and is subsequently used in a series of crimes. Lou Diamond Phillips' character, Agent Ian Edgerton, appears in the series finale.