Sheriff Brock and the rest of the town fears the worst when a local teenaged girl disappears and they arrest her boyfriend, Brian Latham, as a murder suspect. Meanwhile, Jill and members of the community become alarmed when it appears that a teacher is advocating creationism in Matthew and Zach's school.
A Wisconson Federal judge orders that 400 black students from the Green Bay ghetto be bused to Rome's schools, prompting panic among Sheriff Brock and the parents, knowing that a good number of them are lowlifes and drug dealers that come from that neighborhood. Meanwhile, Wambaugh gets a surprising response to his appeal of the Brian Latham murder conviction to go the U.S. Supreme Court in Washington DC. Also, Maxine makes a mess of her relationship with Littleton.
Jill and Judge Nance air their feelings in a heated face-to-face exchange after she is arrested after she reveals of performing surgery on the Christian Science man. Meanwhile, Kimberly has a run with one of Green Bay's transfer students, named Aisha, who initially responds with hostility. Also, Littleton asks Maxine out on a date.
Judge Bone has a troubling case when a social worker takes a young girl from her mother, who practices witchcraft. Meanwhile, Maxine and Kenny seek out Ginny for advice on the occult and learn that she has met an unusual fate. Also, Jill gets some new opposition in her race for mayor who happens to be Carter, and Ed Lawson.
After the innocent Zach gives a school history report which is filled with racist comments, it hurts Jill's mayoral campaign just before a crucial debate and the election. It turns out that Zach got his information from the 1911 edition of the Encyclopaedia Britannica. Both Carter and Lawson take advantage of that to play on Rome and Green Bay's racial tensions. Meanwhile, Kimberly finds herself shunned when she sticks up for Aisha when she's mocked by jealous white students for getting good grades.
An ailing Wambaugh travels with Jill to Chicago for some specialized medical treatment for his liver, where she becomes angered by Dr. Jeffrey Geiger's arrogant attitude. Back in Rome, Sheriff Brock gets upset at an announcement from Kenny and Kimberly that they want to date.
Brian Latham continues to plead his innocence, and everybody starts to doubt his guilt. The real murderer has confessed to Father Barrett, and Judge Bone tricks him into admitting that Brian is not the killer. The really guilty party is revealed.
In this cross-over from an episode on 'The X-Files', the week before Christmas has Sheriff Brock, Kenny, Maxine and other deputies searching a farm when Carter suspects that strange genetic experiments involving cows may be taking place there.
Again, a person is found dead in the home freezer, this time a male masseur, and people fear that a serial killing is in progress. As it turns out, the victim was giving more than just massages to many of the housewives, so the number of suspects increases.
An African-American woman chokes on the microphone and is pronounced dead. She unexpectedly wakes up in Carter's morgue and recognizes him as her soulmate. Kenny and Maxine continue to test out their relationship.
A convicted child molester with a surprising ancestry moves into Rome and has to tell all the neighbors about his past. Wambaugh refuses to take on a client for the first time in his life, but sings Barbra Streisand's "He touched me" with choir and church organ at his funeral.
Sheriff Brock asks Laurie Bey to help him, Maxine, and Kenny look for Mayor Ed Lawson who's missing and wanted in connection to a murder, while Jill and the rest of the town begin the process of finding a new mayor. After Laurie Bey helps with the police to arrest Lawson, she's surprisingly is chosen to be the new acting mayor of Rome.
In the aftermath of Jill's criminal trial acquittal, Judge Bone is asked to run on the validity of a law prohibiting physician-assisted suicide. Meanwhile, Kenny and Carter investigate the killing of some swans at a local pond, and discover their chief suspect is Zack.
Zach is tormented by guilt over the swan episode. He prays in a church, and blood starts to pour from the palms of his hands. His schoolmates want to make him a saint, and the Catholic Church starts to investigate if he really is a stigmatic. After Jesus comes to him in a dream disguised as the late Potato Man, he heals a boy who has leukemia.
Sheriff Brock's attorney father arrives for an unexpected visit and creates tension the Brock household when he makes a seemingly generous offer that angers Jimmy. Meanwhile, Kenny and Maxine try to deal with a rebellious teenager and his loud motorcycle.
After a lowlife teen shoots Father Barrett during an attempted robbery at the church, Mayor Laurie Bey's decision to continue with a planned spring pageant draws fire from Sheriff Brock and the somber townspeople. But a twist comes when Mayor Bey later reveals some surprising news that she happens to be pregnant, and refuses to tell who the father is.