Hooker tries to get something on a criminal whom they have trouble getting anything on. When the informant he sends gets killed Hooker tries to get his ex, a hooker to testify against him. They later learn that the criminal has someone on the inside looking after him, someone he knew since he was a kid. When the safe house is hit Hooker and the girl go on the run. But they have to find some insulin for her cause she's a diabetic.
Hooker and his colleagues take part in a drugs raid at a scrapyard. Afterwards, the body of a policeman is found; he wasn't involved in the raid and Hooker begins to suspect the officer was corrupt. Meanwhile, Stacy, who logged in the heroin seized, crosses paths with her former fiance, a lawyer who (unbeknown to her) has links to the same drugs gang. When he engineers a switch whilst the drugs are in transit to the LCPD laboratory, Stacy is suspended and eventually decides to quit the force. Hooker must solve the case, whilst saving both Stacy's career and her life.
The latest victim of the Marina Rapist - and the first to survive - is known to Hooker, but she resists his request to admit what really happened for fear of losing her boyfriend. Even when one suspect is killed whilst trying to escape a crime scene, Hooker isn't convinced the Marina Rapist's crime career is concluded.
Hooker and the department have been working on getting two Hispanic gangs to settle their differences. But when an attempt is made on one the gang leaders and the ones who did it were wearing the colors of the other gang but the other gang swears they didn't do it. But when more attempts on other gang members are made a war is brewing. Hooker tries to get them to calm down. What they don't know is that an arms dealer wants them to go to war so he can sell them weapons.
Hooker and Romano come across what appears to be a robbery in progress. they go in and when they confirm it, they try to call for back up but some kids who were spray painting take the cruiser leaving them with no way to call for back up. They confront them and eventually Romano is hit and Hooker gets trapped in the elevator with one of them with no ammunition.
Stacey walks in when a robbery is being committed and is shot. They learn that she was shot with bullets that penetrate the protective vests that police officers wear. Hooker is determined to find the one who shot her even if it means jeopardizing his career.
A friend of Hooker's who is working vice is shot and killed. Investigations show that he appears to be on the take. Hooker doesn't believe it and is determined to clear his friend's reputation, helped by a former prostitute.
Hooker works with another cop, who's a friend to get some drug dealers. But during their investigation, they discover that his friend's daughter is not only involved with the people they are looking for but she's also an addict.