While staking out a warehouse robbery, Pete accidentally injures a young woman named Billie. Guilt-ridden, he falls in love with Billie, an aspiring folk singer with a hauntingly beautiful voice. Things become unexpectedly complicated when Billie's brother, Case, is one of the robbery suspects. Case learns that Pete is an undercover cop and, desperate for money, demands that Billie get the goods on Pete to lead them to a big robbery.
Linc receives a desperate call from an old friend, now an inmate at a mental institution. Shortly afterward, the friend is dead of "heart failure", only the latest of a number of strange deaths at the place. Linc goes undercover as a patient at the institution, hoping to find out what's going on.
A hard-nosed ex-cop returns from Vietnam to investigate the death of his brother, who was killed in a car accident just after he called him and told him that he had seen a murder, and that the murderer was an undercover cop.
The trio becomes involved in the case of a young boy who's being raised in an orphanage. His mother is not taking care of him, but she does not want to give him up for adoption, and she is involved with a drug dealer.
Pete is knocked out and jailed in a small town when he tries to assist Levi Frazee, an Indian who is believed to be withholding the whereabouts of his cousin, who is suspected of murder. Later the main witness, the victim's wife, changes her story and claims it was Levi who killed her husband.
Linc comes to the airport to meet a friend who is returning from Vietnam, only to learn that he was killed by a sniper on the day he was supposed to go home. Suspicious of the story of how his friend died, he wonders if any of the four other servicemen in his unit who have returned know more than they are telling.
Julie is staying at a beach house where she is helped by a kind old fisherman who lives nearby. He tells her to ring her porch bell whenever she needs his help. When she visits his house the next day, someone else lives in the house. She can't find the mysterious old fisherman except when she rings the bell, he suddenly shows up. Is he for real or a figment of Julie's imagination?
The head of a local campus ROTC is murdered, and the main suspect is the man's mentally disabled teenage son, whom he had frequently beaten. However, Pete and Linc, who have befriended the youth, believe he is innocent.
Julie is forced at gunpoint to drive Cliff Hansen and his young son to Los Angeles. Cliff has kidnapped his son to take him away from the influence of his wealthy father-in-law. However, both Cliff and his son have been exposed to Rocky Mountain Spotted Fever, and need medical attention as soon as possible.
The trio search for an illegal immigrant, a friend of Pete's who ran after an immigration officer was seriously injured while trying to apprehend him. Complicating their search is a stubborn police lieutenant, who comes from the same Mexican town as the immigrant, and who regards the trio as interfering. The cop, it turns out, may be involved himself in helping people enter the U.S. illegally.
Student activists protesting for academic changes at their college take over the administrative building, and hold Julie and an elderly and ill female teacher hostage. Meanwhile, a seemingly quiet but demented student named Walter has taken their otherwise peaceful fight into fanatical-warlike territory with a rifle and other weapons! It's up to both the men of Mod Squad and the hostages to stop Walter before he kills any more innocent people.
In a reversal of the more common situation, a conventional young friend of Julie's asks the trio's help in locating her father, who has gone into the hippie subculture. Unknown to any of them, he has also unwittingly become involved in a girl's murder, which the trio is also trying to solve.
A businessman reports the theft of his partner's car---and admits that he wired it with dynamite, set to go off in eight hours. Unfortunately, the search for the car is complicated, as the thieves change the plates, and the car changes drivers more than once.
A straight-laced young minister comes to L.A. to investigate the murder of his brother, a doctor who had set up an inner city free clinic for homeless and runaway youths. Many stolen goods were found in the doctor's clinic after his murder, and no one, including Pete, Linc, and Julie as well as the brother, believe he could have been involved in burglary. Linc is assigned to go undercover and accompany the minister in his search for answers.
Greer and another veteran cop have both been frustrated by a drug pusher they've been trying to nail, who has twice had his case dismissed on legal technicalities. Finally, the third time appears to be the clincher, as the man is caught at an airport with a case full of heroin. But then the pusher calls Greer to his cell and insists that he has been framed, and Greer reluctantly agrees that something about the case doesn't fit.
A girl working undercover for a cop trying to bring down a drug lord is accidentally killed. Because of her resemblance to the dead girl, Julie is quickly recruited to impersonate her and continue in the mission, despite the great risk.
The trio tries to help a boy in his search for his father, who came to L.A. from West Virginia hoping to find work. It soon becomes apparent that there are people who don't want them to find the man, and that he is in debt to loan sharks.
A middle-aged legendary prizefighter tries for a comeback match, mainly to please his troubled son, whom he thinks wants him to prove he's not a has-been. But the son may have other reasons: he is in debt to gamblers who want him to give them inside information on his dad's odds. Linc feels that the fighter may be in physical danger if he goes ahead with the match.
While working undercover as safe crackers, Pete and Linc meet a timid, clumsy young man who asks them to teach him about their trade. They learn that the young man has a twin brother who is a successful businessman. What they don't know is that the businessman is actually the leader of the industrial spying ring they are trying to investigate. And that's only the start of the surprises to come.
When his motorcycle breaks down on a trip, Linc stops in an abandoned town, only to discover that a kidnapped boy is being held there for ransom. The kidnappers decide to hold Linc as well until they get the money.