Though To Kill a Mockingbird is told from the perspective of the main character, Scout, and is considered a "coming-of-age" story, I consider the main plot of the story to be the trial and Atticus' defending of Tom Robinson. This is the premise on which Scout builds the rest of her story. In this main plot, the conflict is the fact that a black man is on trial for a crime he did not commit. Because the book is set in the South during the Civil Rights Movement, there is a social conflict concerning Atticus' fair fight in defending him.
Scout's story focuses on the trial, but as a result, the first sub-plot of the novel is the account of her growing up in the two years that the book covers. This sub-plot focuses on the lessons she learns from the other characters as well as the social circumstances of which she is naturally a part. The main conflict(s) in this subplot is the way in which Scout reacts to the world around her. The growing-up sub-plot encompasses the 2nd sub-plot: the story of Boo Radley. He starts as a mysterious fascination for the children at the very beginning of the novel. The conflict starts out as a question of Boo's identity. The ironic resolution to this conflict is that Boo, though a stranger and a social outcast, is the one who saves Scout and Jem from Bob Ewell's attack (which was the result of his anger toward Atticus, leftover from the trial).
All three plots are masterfully woven together through the delicate connections of everyone to everything in the small town of Maycomb.