The first Pretty Little Liars book left off with the discovery of Alison's body and her funeral. All the girls got a text from the mysterious and threatening A:
"I'm still here, bitches. And I know everything."
Flawless, the second book in the series, starts with a flashback to "the Jenna incident." Toby had been peeping in the Liars' window. Alison was affronted and decided to get revenge. She was going to set off some firecrackers outside of Toby's tree house to scare him. Something went wrong, and Jenna was permanently blinded. Toby took the blame for the accident. Alison always said that he kept her secret because she was keeping his secret, but none of the other girls knew what that secret was, except Spencer.
None of the secrets have changed in this book. Aria is still hot for teacher, then hot for Hanna's ex Sean. Hanna still has daddy issues and body issues. Spencer is still chock full of sibling rivalry. Emily still has sexuality issues.
The big event of the book is Foxy, a charity dance thing. Hanna's dad invites her for a fancy weekend, but invites his new wife and daughter. A texts Hanna that Sean is attending Foxy with someone else, and Hanna sneaks away to the event. Sean invited Aria and the two are the talk of the party. Spencer is there with Andrew, her main academic rival. It's obvious that he's smitten with her, but she hurts his feelings by revealing she's attached to her sister's ex. Finally, Emily invited Toby Cavanaugh as her date. When Spencer sees them together, she freaks out. By the time she gathers the others, Emily has disappeared.
The girls think Toby might be A and that he could hurt Emily. During their ride home, Toby suddenly becomes angry and mentions how much he hated Allison. There's a hilarious misunderstood conversation where Emily accuses him of a terrible deed. It's funny because she's referring to killing Alison while he's referring to having inappropriate relations with his stepsister. Well, not funny-haha. Emily thinks that he killed Alison and she runs away from his car. She makes it home safely, though Toby follows her and tries to talk to her. In the morning, his body is found in the woods, dead from a suspected overdose.
Because they think Toby was A, the Liars believe that everything is over. Of course, there's still a whole bunch of books left in the series, so it's not quite as simple as that.