After a senator suddenly dies after completing (and sealing) an investigation into the nuclear power industry, the remaining senator and the state governor must decide on a person who will play along with their shady deals and not cause any problems. They decide on Billy Jack, currently sitting in prison after being sent to jail at the end of his previous film, as they don't expect him to be capable of much, and they think he will attract young voters to the party.

After Billy Jack in sentenced to four years in prison for the "involuntary manslaughter" of the first film, the Freedom School expands and flourishes under the guidance of Jean Roberts. The utopian existence of the school is characterized by everything ranging from "yoga sports" to muckracking journalism. The diverse student population airs scathing political exposes on their privately owned television station. The narrow-minded townspeople have different ideas about their brand of liberalism. Billy Jack is released and things heat up for the school. Students are threatened and abused and the Native Americans in the neighboring village are taunted and mistreated. After Billy Jack undergoes a vision quest, the governor and the police plot to permanently put an end to their liberal shenanigans, leaving it up to Billy Jack to save the day.

Ex-Green Beret hapkido expert saves wild horses from being slaughtered for dog food and helps protect a desert "freedom school" for runaways.

A ruthless motorcycle gang rides into a California town and terrorizes its denizens.

Billy Jack returns to bring down a child pornography ring headed by the Godfather of Godfathers. The Return of Billy Jack is an unfinished theatrical film that was in production from December 1985 to early 1986 in New York City with additional scenes filmed in Toronto.