The second season of Numbers, an American television series, premiered on September 23, 2005, and its season finale was on May 19, 2006. Season two sees several changes to Don's FBI team: Terry Lake is reassigned to Washington DC and two new members join Don and David Sinclair: Megan Reeves and Colby Granger. Charlie is challenged on one of his long-standing pieces of mathematical work and also starts work on a new theory, Cognitive Emergence Theory. Larry sells his home and lives 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 working and dating again, though he struggles with the loss of his wife.
When a judge's wife is shot dead while arriving into her parking garage, Don and his team look into the judge's cases to determine if one of his verdicts led to the murder.
First appearance of: Diane Farr as Megan Reeves and Dylan Bruno as Colby Granger
The FBI becomes involved in the stalking of a popular singer after she is threatened by an intruder in her house and reveals a series of threatening letters she has received through the mail. Charlie receives an anonymous love letter from someone other than Amita.
Don and Megan are called to the murder scene when the CFO of a powerful energy company—who was about to testify against her fellow executives—is murdered at her home and her son is the only witness.
Along with David Sinclair and new FBI Agent Colby Granger, Don discovers a secret code during a raid and enlists Charlie's help to crack it. Charlie cancels his date with Amita only to discover she already made other plans for that night.
A week-long series of counter-terrorism exercises are put to the test by Homeland Security in Los Angeles, but the first one is violated by someone who releases a potentially lethal gas in the subway system. Alan hosts a wedding for a girl from the Eppes brothers' past.
Don investigates a series of home invasions in which the thieves steal only high-end items from wealthy individuals. Meanwhile, an old adversary challenges Charlie's work.
Megan feels personally responsible for an agent's death following an explosion at a house where meth is being illegally produced and that the FBI targeted for a bust but the case takes a new direction after Charlie discovers that the drug kingpin was in the FBI office, looking for help in rescuing his supposedly kidnapped daughter.
An arsonist believed to be part of an extremist environmental group sets a fire at a car dealership that kills a salesman. The group's name is spray painted at the scene and is the fourth such fire, but the first to claim a life.
First appearance of: Sophina Brown as Bianca Styles, before she is cast as Nikki Betancourt in season five.
When Don and his team are called to the murder scene of a Los Angeles gang member, they learn the victim is a fellow agent who had been working undercover.
When the FBI is called to investigate a murder at a Los Angeles card club, it leads the agents to unravel a complicated card counting scheme involving a group of college students whose lives may now be at risk.
A South Asian teenager is found in the blood-spattered basement of an old downtown hotel where she was apparently being tortured. The investigation soon reveals that the girl, along with three other missing women, are victims of a black-market organ-harvesting scheme.
A DNA synthesizer with the capability of customizing diseases is stolen from the campus where Charlie teaches, and Don figures the thieves may be terrorists out to start or advance a bio-warfare program.
A pedestrian is killed when a homemade bomb explodes under a car outside of a downtown Army recruiting center. The investigation reveals that a similar bombing that killed two people occurred exactly 35 years ago at a ROTC office. Things take a turn when Don discovers that his father was a member of an anti-war group believed to have been associated with the bombings.
When the bodies of three illegal-immigrant women are found on government-owned land in a wilderness area, Don investigates and learns a psychic led the police to the crime scene after allegedly seeing visions of the bodies. Charlie becomes extremely annoyed after learning that Don is using the psychic's help to solve the case, maintaining that true psychics do not exist.
In an effort to find the murderer of an Iraqi woman, Don enlists the help of the victim's cousin, who lives in Los Angeles. Through her cousin, Don learns information about the woman's disturbing connection to Saddam Hussein, which could lead to her murderer. Meanwhile, Charlie reunites with an ex-girlfriend, a best-seller neuropsychologist.
As Don and his team investigate the motive behind two students's deadly school shooting, Charlie uses the school's radio frequency identification system to track the shooters's movements through the school's hallways. But the team are stunned when Charlie reveals that they're looking for a third shooter, someone with motive.
When an ATF agent is found dead amid questionable circumstances, Don demands to take on the case, which revolves around an elaborate bank heist, after he learns the victim is his ex-girlfriend.
After an unknown man opens fire in the FBI offices, causing carnage and destruction, Don and his team must investigate his motive and his connection to a dangerous arms dealer who is on trial. Meanwhile, Don soon learns that the bullet that killed the sex offender the team interviewed came from Colby's gun, forcing Colby to be put on desk duty for the time being.
An FBI investigation into a computer hacking scam, which taps into a bank's system to gain access to customer's identities and financial assets, becomes personal for Don when the Russian mob spearheading it comes after him and threatens the safety of Charlie and Alan.
Two women are found dead with an apparent drug overdose, in similar positions with a syringe in the left arm; Don suspects a serial killer. The investigation reveals valium (diazepam) and morphine. Charlie's help on Don's case is hindered by his bizarre dream about his mother.
