On her way home one night, a female radio talk show host witnesses a woman being murdered by an arms dealer. As the killers are about to shoot her too, T.C. saves her and fires back at the killers - but the flash from his gun blinds the woman. His guilt over this, and the fact that she bears an uncanny resemblance to the love of his life, Chris Kelly, leads T.C. to become obsessed with protecting her. This leads to romance - the victim thinking he is just a caring cop, not the one who robbed her of her sight. Matters become compounded as her sight begins to return.
Jamie Strickland's sister, Jennie, a witness in a previous homicide case, returns from hiding. Detective Marcus, the dirty Narc, is on the warpath, and the juvenile shooter that Jennie can identify has escaped from a work camp as well.
Russ and Cory enter the ugly, violent world of white supremacy to catch the racist killer of several local Mexican and African-American young men. Simultaneously, Jamie tries to protect a young boy, whose talent for photography puts him in jeopardy when he unwittingly captures on film a clandestine meeting between two powerful adversaries.
After Russ and Bobby arrest a murder suspect, the trial lands before hanging Judge J. Gunnar Halloran. After tossing the weapon because of an illegal search, the heat is turned up on Bobby and Russ, who are accused of planting evidence. The case is further hampered by the fact that Judge Halloran has fallen in love with the exotic dancer sent to blackmail him into releasing the defendant.
Bobby Cruz' sister, Teresa, witnesses the suicide of a high school classmate and begins to fall under the spell of the girl's manipulative boyfriend. An ambitious rookie cop, recently assigned to Pacific Blue, turns out to be a spy for Internal Affairs. Things get complicated when he's let into the young Pac Blue officers' scheme to frame a ruthless drug dealer.
Cory learns she is pregnant, but is unsure whether the father is T.C. Callaway, a one night stand, or Will Blake, her District Attorney boyfriend. Before she can tell either one, she's kidnapped by two jewel thieves who offer to let her go in exchange for the release from jail of their ace safecracker, who happens to be a crazy, violent, female bodybuilder (played by WWF superstar Chynna). T.C. is shot in the leg while saving Cory McNamara.
T.C., now hooked on painkillers from being shot in the leg, leads Pacific Blue on the trail of a potential serial killer who preys on young runaways that he locates via the Internet. Cory and Monica convince a woman psychic, who used to help the police back East, into helping on the case.
While Russ, Bobby, Monica and Jamie are out tracking pot growers in the Santa Monica mountains, Chris Kelly returns to visit a wounded T.C. Callaway, who's fighting addiction to pain pills, as well as kidnap victim Cory McNamara. All hell breaks loose when Chris finds out T.C. slept with her best friend, Cory, and that Cory doesn't know if her pregnancy is the result of Will Blake or T.C. Callaway. The season-ending cliffhanger occurs when Cory opens the blood test results to find out which one is the father.