The main themes are how unfair the criminal justice system can be, and how the rich have power to hurt others. The main character and narrator, Caleb, is falsely accused of a crime by an angry gentleman, Mr Falkland (a murderer), and spends over 270 days in jail in awful conditions before his trial. During this time he is badly mistreated including having a manacle very painfully put on his swollen, twisted ankle and having the straw for his bedding taken away in case he might conceal something in it.
Caleb escapes from jail, but never escapes from Falkland's power. He's tracked down and everywhere he goes his reputation is ruined and the threat of prison looms over him. Later he is acquitted at his trial but Falkland continues to harass him. Falkland hires a man to track him down wherever he goes, and also to assault him if he tries to set sail for a foreign country. Being innocent does Caleb little good as he feels from place to place and the people he meets turn against him, often without even being willing to listen to his side of the story.
The kindest characters to Caleb are a band of thieves who have a sense of honor and expel one of their own for assaulting Caleb (this brutal former thief is the man Falkland later hires to track Caleb).