Puppeteer opens with a D'Haran soldier giving Darken Rahl a box of Orden. We discover that he now has two of the three boxes. He tells the soldier to tell Queen Milena that he excepts all her demands in return for the third Box of Orden. The solider asks why they don't just destroy her and take the box, and Rahl says that when he has all three boxes he will have unchallenged power and her demands will be meaningless.
Richard and Kahlan are standing overlooking Tamarang, Queen Milena's city. Kahlan reveals that Queen Milena is ruthless and once killed many people for a small jewel. Zed comes up and tells Richard and Kahlan that a Emissary for Darken Rahl is coming for the box the next day. Zed tells Richard and Kahlan to delay the emissary, while he breaks into the castle as an entertainer for Princess Violet's birthday to steal the box.
Princess Violet turns down entertainers, and after Zed's act she chooses him as her entertainer. Zed introduces himself as Ruben Rybnik, Master Puppeteer. Violet shows Rachel to Zed, a girl she got for her last birthday to practice ruling over. Zed proceeds to trick Princess Violet into showing him that she has a key to the treasury where the box of orden is.
Richard and Kahlan see one of Darken Rahl's scouting parties. They decide to attack the soldiers and have Kahlan confess one of them so they can make him send a message to Darken Rahl to delay him. Richard ends up killing all the scouts and Kahlan gets mad at him for being over protective. She finds a journey book on one of the men. She explains that the journey book is how Rahl communicates with the scouts. Richard and Kahlan plan to use the journey book to kill Darken Rahl.
Rachel steals the key to the treasury from Princess Violet for Zed. Zed manages to steal the box of orden. Zed plans to take Rachel with him, and while they are leaving they are caught by the queen in the hall and Zed gives Rachel the box after forcing her to hide. Rachel goes to the kitchen before leaving to get a loaf of bread to hide the box in. When Rachel is in the kitchen Princess Violet comes in and Rachel hides the box in the cake mix. The cook puts the cake in the oven, with the box inside.
Richard and Kahlan are lying in wait with a crossbow to shoot Darken Rahl. When he rides over the hill Richard realizes that it is a double and Rahl must have realized it was a trap.
Darken Rahl is already at the castle. Queen Milena asks Darken Rahl to do them the honor of cutting the cake, which has the box of orden baked inside. Zed tries to buy time by doing the puppet show before the cake. Rachel makes to get the box and escape while Zed puts on the puppet show.
Darken Rahl goes to the treasury and realizes that the box there is a fake. He orders his guards to get Zed. Darken Rahl reveals that he knows that Ruben is really Zed, a first wizard.
Rachel is running through the woods with the box when soldiers start to chase her for the box. Richard and Kahlan come in and save Rachel.
Darken Rahl is furious and cuts of Zed's head. It turns out that he was just a puppet and Zed is okay. Zed meets up with Richard, Kahlan and Rachel. Rachel goes to live with one of the cooks, Martha.
Darken Rahl kills Queen Milena, and writes a message in the journey book. I will find you.