The following version of the book was used to create this study guide: Hardinge, Frances, The Lie Tree. Amulet Books, New York, NY, 2016. (Originally published in Great Britain in 2015 by Macmillan UK.) Kindle AZW file.

Faith Sunderly arrives in Vane with her parents, Erasmus and Myrtle, her younger brother Howard, and her Uncle Miles. Faith quickly learns that the family trip was not just a chance to accompany Erasmus on one of his archaeological digs. It is an effort to outrun the scandal that is threatening her family's social standing and her father's standing as an expert in the natural science field. When Faith is forced to admit to Erasmus that she had gone through his letters, her father is furious and makes it clear that a daughter is worthless to a family. In an abrupt change, he asks Faith to help him make a dangerous trip by rowboat to a cave. Faith rushes to do his bidding, though she knows their lives are in danger during the trip. Erasmus leaves a mysterious plant in the cave and asks Faith for another favor. She is to hide the fact that she was out of the house with him and say they talked in his study until after midnight. Erasmus then leaves again, and Faith rushes to cover all signs of her nighttime activities.

The next morning, Faith learns that Erasmus never returned. She finds his body in a tree, and it seems that he might have jumped from the cliff to his death. Myrtle rushes to hide the possibility that Erasmus committed suicide because she knows they will forfeit all his money, leaving the family destitute with no way to survive. Faith believes Erasmus was murdered, and she quickly gathers his personal papers in the hope of finding out who killed him and why.

Faith discovers that Erasmus first learned about the Mendacity Tree from another natural scientist, a man named Hector Winterbourne. Hector died in prison after telling Erasmus where to find the tree. Faith learns that Hector's widow is now living in Vane, married to the local magistrate.

To get to the truth, Faith decides to use the Mendacity Tree. She begins by telling the tree a significant lie about Erasmus's ghost restlessly haunting the house. She helps the lie along by planting some evidence and is rewarded when she returns to the cave to find the tree has produced a single fruit. She has a vision from that fruit and sets out to create another lie in the hope of finding the identity of the killer. As her lies seem to become fact and the people of Vane look at the Sunderly family and each other with distrust, Faith finally comes to the truth.

Faith sets out to prove that Agatha Winterbourne Lambent was involved in Erasmus's murder. She believes she will prove that Agatha played the supporting role and that her husband, Anthony, killed Erasmus. What she discovers is that Agatha is an avid natural scientist who has always had to work under the guise of supporting a husband, first Hector and now Anthony, and that she is willing to do anything to recover the tree Erasmus stole from Hector. Agatha is helped by a gentle man named Ben Crock. Agatha saved Ben from certain death once and he is willing to do anything for her, including killing those who get in her way. Agatha is so determined to get the tree that she kidnaps Faith. Once they are inside the cave, Faith manages to escape, shedding light on several limbs of the tree in the process. Light (truth) always destroys lies, and the tree goes up in smoke.

Agatha, under the thrall of the smoke from the tree, throws herself off a cliff. Ben is arrested. Anthony, realizing how he had been deceived by the wife he loved, begins to destroy her samples. Then, he decides to give them to Faith instead. As Faith, Myrtle, and Howard leave Vane bound for home, Faith realizes that the ruthlessness she has seen in her mother is nothing more than a woman trying to defend herself and provide for her family in a world that does not value women. Myrtle also reveals that she knows Faith will follow her passion into the natural science field. She does not berate Faith for it, even though she knows those choices will sometimes make life more difficult for Faith.