Documentary tracking the exploits of aging Calvinist preacher Fred Phelps, a convicted felon who leads his cult (primarily composed of his wife, nine of their children, and his fifty-two grandchildren) on their "love crusades" across America, which include calling for gays to be killed, praising terrorist attacks, mocking mourners at the funerals of AIDS patients and murder victims, and literally dancing and spitting on the graves of his enemies.

Following up on his 2007 documentary, The Most Hated Family in America, Louis Theroux returns to Topeka, Kansas, for a week-long visit with the Westboro Baptist Church. He again joins the Phelps family on their controversial pickets where they try to antagonise communities with offensive slogans and anti-gay placards. But four years on from Louis's last visit, there are signs of disarray in the Phelps clan. A series of defections of family members has shaken up the church.

Louis meets the Phelps family — the people at the heart of the controversial Westboro Baptist Church. The Phelps have rabid anti-homosexual beliefs, and often campaign at the funerals of American soldiers. They believe that every tragedy in the world is God's punishment for homosexuality.

Keith Allen visits Westboro Baptist Church to confront them about their extreme religious beliefs.

Louis returns to visit the Westboro Baptist Church in the wake of the death of its leader.

Stained Glass Rainbows explores the most controversial subject facing America today: the collision between the LGBT community and the Christian church. Can gays be Christian? Is homosexuality a sin? Is there a gay gene? Is there such a thing as an ex-gay? Both families and churches are being torn apart over these divisive issues. Stained Glass Rainbows brings together the voices of the left, the right, the middle, and helps bridge the gulf through its dialogue. From gay pride parades to anti-gay protests, Stained Glass Rainbows confronts the controversy of faith through the hearts and minds of people on both sides of this uncivil war.