Don is on the trail of a criminal couple consisting of a 30-year-old teacher and a 17-year-student who are committing crimes across the country. Charlie and Amita's relationship changes and Alan decides to move out. The episode ends in a cliffhanger with Crystal Hoyle, the 30-year-old teacher, taking Megan hostage.

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Mathematics used: Pursuit curves and geodesic sphere

The team jumps into action after learning that Crystal Hoyle has taken Megan hostage and work against the clock and ever-decreasing odds to save Megan before it's too late.

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Mathematics used: Polar spirals and parametric equations

A famous Nazi-looted painting is stolen from a museum and a related murder surfaces.

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Mathematics used: Linear diophantine equations, curvelet analysis, Craquelure and discriminant analysis

The death of a Chinese interpreter outside a nightclub who was knocked down and fatally injured by a car at first appears to be an accident but Charlie's theory later suggests that it was murder and the resulting investigation leads Don and his team to investigate a possible mole from within the Department of Justice. Colby covers up information on Don's case for a friend (Shawn Hatosy) and is left stunned when he finds evidence suggesting that his old friend is the mole that Don and the team are looking for. Charlie is upset when Larry publishes a paper without his help.

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Mathematics used: Steady Motion Algorithm, Curtate cycloid, symmetry and combinatorics

A series of violent highway attacks which appear to be random leaves Don and his team deeply puzzled.

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Mathematics used: Randomness, partial differential equations and traffic flow

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

First appearance of: Aya Sumika as Liz Warner

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Mathematics used: Probability, arbitrage betting and data mining

After an attack on a power station which left parts of Los Angeles in the dark, the team must find the assailant's real target.

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Mathematics used: Set Theory, Center of mass, harmonic series, directed graph, Load flow analysis and Dantzig-Wolfe Decomposition

A minor league baseball player is found dead of steroid abuse, leading the investigators to an unusual chain of suspects. Jay Baruchel portrays Oswald Kittner.

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Mathematics used: Sabermetrics and Shiryaev-Roberts change-point analysis

Mysterious cancer clusters are found around a number of elementary schools whose playgrounds were all paved by the same company. A new CalSci administrator annoys Charlie and his colleagues, while Alan dates her.

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Mathematics used: Groundwater flow equation, cancer clusters, seismic tomography and Kac–Moody algebra

A California State Senator and a psychiatrist—neither have much in common with the other except for one thing...they both turn up dead on Don's watch. While the circumstances of their deaths are different, Don thinks the two murders are related, and tries to prove his hunch right. What he finds may bring to light a deep secret the government has been hiding for years.

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Mathematics used: Network flow, network theory, Euclid's Orchard and target selection theory

Don and Charlie track a killer who has murdered several sex predators. The predators took advantage of teenage girls they met in chat rooms. Meanwhile, Larry is ready to begin an adventure with NASA.

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Mathematics used: Statistical Textual Analysis and principal components analysis

Don, Charlie, and the team search for a polygamist who is on the FBI's Ten Most Wanted List for rape and murder.

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Mathematics used: Lévy flights, Inbreeding coefficients and kinship chains

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.

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Mathematics used: Fluid dynamics, constraint and optimization

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 to help him deal with the aftermath of the Crystal Hoyle Case.

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Mathematics used: Outliers and data mining

Don and the team reopen a cold case when a bunch of kids playing in an abandoned empty construction site discover a police badge. When Charlie joins the investigation, they attempt to track down the owner of the badge, a police officer who has been missing for seventeen years but when the team discover that the dead cop was on his way to Internal Affairs, the investigation takes a turn. Meanwhile, Alan is informed that he's being sued.

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Mathematics used: Laser Swath Mapping and quantum mechanics

One of David's closest friends is called into question after a man dies during a mixed martial arts sparring match. When it turns out that this is not the first time such an event has happened, things look even worse. Charlie is busy practicing what little he knows about poker, so he can take Larry's spot in a tournament.

Mathematics used: Kruskal's algorithm and Flow network

Don talks to his therapist 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.

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Mathematics used: 'Cake-cutting' algorithm, logic maze and state diagram

Several area murders seem to be tied to voter fraud. Don, Charlie, and the team must find the killers before they strike again.

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Mathematics used: Statistics, probability theory, metadata and organizational theory

When a jet crashes in the middle of a forest, Charlie suspects that there is more to the crash than meets the eye.

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Mathematics used: Ito-Stratonovich drift integrals and wavelet deconvolution

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

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Mathematics used: Explosions, paradigm shift, coherence and outliers

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 while Larry returns from his NASA mission.

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Mathematics used: Probability theory and tit for tat

Don, Charlie and the team take on an unknown group of terrorists who may be using nerve gas to undermine the city's water supply.

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Mathematics used: Social network analysis

$50 million dollars in medical relief is stolen. Someone other than the FBI wants to recover the shipment. Don and the team find themselves being pitted against blackmarketeers in a race for the supplies.

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Mathematics used: Greedy algorithm and Dijkstra's algorithm

In the wake of a deadly standoff with a mysterious, yet brilliant bomber, Don and Charlie discover that he was poisoned to keep him from exposing a secret while the team are left reeling and stunned after learning that one of their own is a traitor, a revelation that threatens to change the team forever...

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Mathematics used: Merkle-Hellman, Wheat and Chessboard Problem, straddling checkerboard, substitution cipher, Bacon's cipher, knapsack problem and Lorentz force