"Blues for Mister Charlie" is the story of a black man killed by a white man and the court case that follows.

Lyle and Jo are a married couple and local shop owners. One night, Lyle kills Richard—a black man— by shooting him after they get into a fight at Lyle's shop. Richard was unarmed because he gave up the gun he was carrying when his father convinced him to do so.

Richard's father Meridian is the local pastor. He's teaching a group of black people when Parnell comes to tell him that his son was killed. He's a nonviolent man who advocates that other black people avoid violence even in response to the violence of white people. He trusts that God and the justice system will do right by his son; as he sees both systems fail him, he begins to change and place his faith in armed resistance.

As the trial continues, various people lie on the stand. Parnell, the editor of the paper and a man who is friends with both Lyle and Meridian, waters down his testimony because he doesn't want to suffer social consequences by going against Lyle. Even if everyone had told the truth, it was unlikely that Richard would have received justice. Black people weren't even allowed to be jurors. Lyle even had a history of murdering another black man in the past—the husband of a woman with whom he was having an affair. Still, people conspire to protect him.

Lyle is found innocent and both Parnell and Meridian are changed by the trial. Parnell leaves his weak commitment to equal rights for black people behind and joins a protest march. Meridian puts aside his nonviolent views and obtains a gun. After losing both his wife and son to racially-motivated violence, Meridian is more committed than ever to getting justice no matter how he has to do it.