Criminal Jack "Sonny" Walker is terrorizing the city with violent armed robberies. During one of those robberies one of the gang members gets hurt and Sonny kills him so he can't confess to the cops. The police decide to infiltrate the burglars and set up a meeting between officer Jack Shaw and Sonny. During the undercover assignment Jake's loyalty is tested in a way that could compromise the whole team.
Jake and Alex have to bust a burglar gang whom stole millions worth of heroine from police storage. Meanwhile Sonny receives a visitor in jail from his ex-girlfriend who tells him how Carlos Cortez helped the police. Sonny makes Cortez pay for what he has done. Alex struggles with her feelings for Carlos now she knows John has an eye on her.
After the unexpected death of John, CIA Agent Frank Donovan takes control of the team. Alex and Jake aren't to trilled about it but don't get any time to complain. The 7-year old son of public prosecutor William Murphy was kidnapped by the dangerous drug dealer Alejandro Ortega.
Jake and Alex go undercover in 2 rival drugs gangs. Jake becomes a part of power full drug dealer Quito Real's security team and Alex goes undercover as bouncer from an escort agency. Quito wants to cooperate with the Chinese gang from Benny Li, to some people's dislike. Meanwhile Carlos Cortez is being released and plans Sonny Walker's escape from prison.
Frank Donovan's team looks for a gang who stole a lot of diamonds, one of them being the rare and very valuable "Hope"-diamond. Alex pretends to be a buyer of the stones and is able to contact the thief Michael "Mick" Vincent quickly. Meanwhile Jake has difficulties to testify against gangster Quito Real and makes a deal with Sonny Walker which could help get him out of prison.
Sonny Walker robs a protected car which is transporting special paper used to create money. Together with forger James Wheel and Quito Real he wants to counterfeit a lot of money. In addition Sonny still holds a grudge against Jake who was the cause for his short imprisonment. Meanwhile Alex and Carlos Cortez discover that they are attracted to each other.
Jake infiltrates a corrupt Elite Police-Unit who operates in a dangerous city area. Some of these cops have a violent way of getting things done and make trouble with everything that stands in their way. Jake has to find out which of the members are involved. Alex is also put on the case, she pretends to be someone from internal affairs.
Jake and Alex are working undercover in a prison to expose a few corrupt security guards when suddenly an uprising breaks out. They are kept hostage together with the security guards and are in the hands of the good will from the prisoners. Frank tries to do everything to free his 2 team members, but the prison director doesn't agree with Frank's methods.
Jake infiltrated in a gang and robs a bank with them. During the robbery something goes very wrong and Jake is shot. The robbers are holding all the customers hostage. Frank tries to negotiate with them but without luck. Meanwhile Jake tries to calm things down inside to prevent any further victims.