Tom Robinson is a black accused of raping a white woman. In Maycomb, there is no way he will get a fair trial. Atticus knows this, but Jem still believes in justice. Throughout the entire trial, Jem believes that Tom will be found innocent.
Atticus does his job in proving there was no way that Tom was guilty. Jem is sitting in the balcony with the other black people, waiting for the jury to come back. Scout is there with him as well. When the jury comes back, the judge starts polling them. One after the other repeats "guilty". Jem is stunned. He slumps in his seat. He never thought Tom would be found guilty. He runs out of the courtroom and cries.
What is interesting about his reaction, is that, it is the culmination of everything Jem believed to be true, and he is now finding out they are not true. In a way, Jem has lost a very important innocence of his childhood. He will never again look at his town the same way. He won't ever think of his neighbor's in the same way either. Jem was so sure his father was going to win. Jem now has lost the gift of ignorance about social issues. Atticus wanted so badly to protect his children from the ugliness this trial was going to bring. In the end, however, he is unable to do this. Jem and Scout have forever been changed and shaped by these unfortunate events. Harper Lee had such a way of showing us how ugly people can truly be.