In each Harry Potter book, the 'bad guy' seems to make their appearance in Chapter Thirteen!
Sorcerer's Stone - Professor Snape threatens Professor Quirrell, who we think is a decent man for resisting Snape. We soon discover that Professor Quirrell has joined with Lord Voldemort.
Chamber of Secrets - We learn about T.M. Riddle, which stands for Tom Marvolo Riddle, and is an anagram for I Am Lord Voldemort. We thought at first that Tom was a good person because he led us to believe that he had captured Hagrid with the creature from the Chamber of Secrets.
Prisoner of Azkaban - Wormtail, or Peter Pettigrew, fakes his death by hiding, making everyone believe that he had been eaten by Hermione's cat, Crookshanks. Of course, he's a rat, so how could we have thought there could possibly be anything wrong with him?
Goblet of Fire - 'Mad Eye' Moody, or at least, who we think is 'Mad Eye' Moody, makes his appearance, and turns Draco Malfoy into a white ferret, leading everyone to believe that he's a cool guy. A little Veritaserum, and short supply of Polyjuice Potion help reveal the truth!
Order of the Phoenix - Harry has detention with Dolores Jane Umbridge, and at no point during the book could anyone have thought that she was even remotely close to being a nice, caring, or loving person.
Half-Blood Prince - Harry and Professor Dumbledore go into the Pensieve and see the first meeting of Professor Dumbledore and Tom Riddle (who is already showing his 'Dark Lord' tendencies) at the orphanage.