The primary protagonist in Wizard's First Rule is Richard Cypher, a young woods guide. Richard lives in an area of the world known as Westland, which is the only part of the world that at the time contains no magic. The Westland is separated from the other lands by a dangerous magical boundary that prevents anyone without the aid of powerful magic from passing through it. On the other side of the boundary are many sovereign nations, jointly known as the Midlands, and farther still past another magical boundary lies the empire of D'Hara. Richard works as a woods guide leading important political figures through dangerous forests, while his brother's interests lie entirely in politics.
Richard is compelled to investigate the unsolved murder of his father, who worked as a trader of ancient artifacts. Investigating the only clue he has, a small piece of vine, he happens upon a woman named Kahlan Amnell, whom he helps keep alive as she is being hunted by a group of four men sent to assassinate her.
After Richard helps to save Kahlan's life, it is revealed that Kahlan has come through the boundary with the aid of five wizards searching for the First Wizard, who is rumored to have crossed into the Westland after the creation of the boundaries. Richard takes Kahlan to his best friend and mentor, Zedd. Arriving, Richard collapses after showing Zedd his vine piece, and Zedd rocile, saying its a snake vine.
When Richard wakes up the morning after being healed from the bite by the snakevine, he names Zedd as the First Wizard, and this is when Zedd names Richard the Seeker of Truth because this was his final test. The "Seeker" is a title which comes with many responsibilities, primarily the Sword of Truth: an ancient magical weapon forged by the powerful wizards of old to enhance the righteous anger of the Seeker of Truth. Zedd explains that while the Sword is an awesome tool, Richard himself is the true weapon. They begin their journey together to stop Darken Rahl, the ruler of the eastern land of D'hara, and prevent him from opening the boxes of Orden: magical devices which can give absolute power over life and death. Kahlan tells them that Rahl has two of the boxes but requires the third before he is able to make the magic work. Richard and Kahlan are tasked with finding the third box and keeping it out of Rahl's hands until the winter solstice, at which time, unless Rahl opens a box, his life will be forfeit to the magic of Orden.
However, due to an attack from some of the creatures of the boundary, Richard and Kahlan are forced to leave their companions in the care of Adie: a mysterious bone woman and cross the boundary alone. They journey to the village of the Mud People. This tribe had the ability to contact spirit ancestors for guidance. In order to seek out where the third box of Orden is hidden, they ask for the ancestors to be contacted. Overnight, Kahlan and Richard share a passioante moment, and Richard asks what a Confessor is, ending the moment. After finally convincing the Mud people to comply by becoming mud people themselves, they learn through a gathering of the mud people's ancestors that only the witch woman Shota, who is more feared than any other person in all the Midlands, has the power to reveal the location of the last box of Orden. While in the gathering Darken Rahl slaughters several mud people and kidnaps Siddin, the son of an elder.
Richard and Kahlan travel to Agaden Reach where Shota tells them that the last box is in the hands of Queen Milena. Kahlan finally tells Richard that a Confessor uses the power of love to destroy a persons mind, making them absolute slaves, able to even die at the Confessors request. Shota also warns Richard that both Kahlan and Zedd will use their powers against him. From Agaden Reach, they travel to Tamarang, seat of Queen Milena, meeting back up with Zedd along the way.
Upon reaching Tamarang, they discover that the last box is gone and eventually realize it was given to a small girl named Rachel for safekeeping. Soon Richard is separated from the group and he falls into the hands of a Mord-Sith named Denna and brutally tortured for a month. However, his innate gentleness alters their relationship, and Richard eventually breaks free of Dennas control after Denna brings Ricahrd to Darkhen Rahl to recite the Book of Counted Shadows. Knowing that Denna has to die, Richard turns the blade of the Sword white through the power of his love and kills her. After helping a dragon named Scarlet find her lost egg, he discovers how to both beat Rahl, and be with Kahlan. Kahlan, falsely thinking Richard dead by Rahl, enters the Con-Dar, or Blood Rage. Thinking Richard is in fact Rahl, she uses her powers on him. Rahl, thinking Ricahrd is now at his mercy, uses him to recite the Book of Counted Shadows. In the end, Rahl opens the wrong Box of Orden, under Richard's false guidance, thus killing Rahl. Kahlan, alone by a pool, orders Richard to leave, thinking he is still under her power, and Richard reveals he was protected, by his already complete and unconditional love for her.
Finally, it is learned upon Rahl's death that Rahl raped Zedd's daughter, which resulted in Richard's conception. Thus, Zedd is Richard's grandfather, and Richard is the new Lord Rahl. Kahlan and Richard set off for the Mud People's village to return Siddin to his parents.