Assassin's Apprentice is a fantasy novel, the first in the Farseer Trilogy, which tells the story of Fitz, a royal bastard who is selected by the King to train as an assassin. Fitz also possesses the Wit, a magical ability which allows him to bond telepathically with animals, a skill which is feared by society. The narrative follows Fitz's experiences as he grows from a child into a young man, chronicling his training and his quest to make a place for himself in the world as he navigates dangerous royal politics.
The novel covers the early life of FitzChivalry, a royal bastard living in Buckkeep Castle as he begins his training as an assassin and successfully safeguards the throne from his over-ambitious uncle Regal, almost at the cost of his life.
The story opens with six years old Fitz being marched by his maternal Grandfather to the Farseer's army base in Moonseye, the Six Duchies' outpost on the borders of the Mountain kingdom, currently under the command of Prince Verity, the second Son of King Shrewd. At the door he is given to a soldier, who is told that he is King-in-Waiting Chivalry's bastard son. The soldier brings him to Prince Verity who orders that he be given into the care of Burrich, Chivalry's own stableman and man at arms. With Burrich, Fitz travels to Buckkeep, the seat of the Farseers. In order to protect Fitz by not allowing them to be associated through contact as well as through blood, his father Chivalry abdicates from the post of King-in-Waiting and with his wife the Lady Patience retires to the royal holdings of Withywoods before Fitz arrives. Fitz never recalls that he met Chivalry, but develops a bond with his father's brother, Verity. Chivalry and Verity's younger half-brother, Regal, despises Fitz and treats him badly when he can.
Burrich, his father's right-hand man is left with the care and raising of the newly named FitzChivalry, which he does as best he is able, taking Fitz on as a stable boy. Fitz quickly learns his duties and for a year or so lives with Burrich caring for the animals in the stables. Fitz, however, is lonely, and becomes a close friend of a young dog named Nosy. Fitz possesses what is known as "The Wit," an ancient and distrusted magic which allows him to bond telepathically with animals, he 'bonds' with Nosy and the two become fast friends. Burrich, however, discovers Fitz's bond and with apparent disgust takes Nosy away, thus breaking the bond. Fitz believes him to have killed the dog, and afterwards is much more fearful of Burrich, believing his life just as easy for Burrich to take. The only other companionship Fitz finds is with children living in Buckkeep town— in particular, a girl called Molly who is two years his senior.
Eventually Fitz agrees to become a "King's Man" to King Shrewd and is bound by oath to serve the king. He is taken into King Shrewd's service and moves into the castle proper. Here he is schooled and is taught basic combat skills by Hod, the keep weaponmaster. One night he is also introduced to a recluse named Chade, who is a skilled assassin. Fitz agrees to learn Chade's skills as he is desperately lonely and seemingly has no other prospects. So during his childhood he is taught the ways of an assassin. He shows great talent in his duties and is able to complete the minor tasks given to him by the king. Meanwhile, news comes from Withywoods of Chivalry's death - it is said that he was thrown from a horse, but it is strongly suspected that Queen Desire, King Shrewd's second wife and Regal's mother, has had him assassinated.
As Fitz is growing up at Buckkeep, the coastal regions of the Six Duchies are being attacked by Outislanders known as the Red-Ship Raiders. The Raiders rampage through villages and towns, killing and taking hostages while stealing little, making their attacks seem to lack a motive. The hostages are returned, reduced to an animal like state with little memory of their former lives. Fitz, when he encounters these returned hostages, finds he cannot sense them with his Wit at all. This stripping away of people's humanity is named after Forge, the first village to be raided in such a way. Later on these Forged Ones become robbers and thieves that start to plunder the countryside, putting another burden on the Six Duchies.
Fitz is eventually made part of a class of students to be taught the Skill, a magic which allows its users to share thoughts and strength. The teacher, Galen, despises Fitz while curiously revering his father (it is revealed later in the book that Chivalry imprinted a false loyalty on him, using the Skill, in a fit of rage). During the classes, Galen treats Fitz without respect, referring to him as "Bastard." Eventually he tries to kill Fitz, then, with more success, tries to sabotage his Skill training. During the last test of Galen's Skill classes, Galen sends Fitz to Forge, ostensibly to see if he can use the Skill to get back. The area is infested with Forged Ones, and Fitz is attacked, although he manages to return safely. While he is away, a stable hand in league with Galen attempts to assassinate Burrich. During this event, Smithy, the dog Lady Patience gave Fitz, and with whom Fitz is Wit-bonded, is killed.
Towards the end of the book Fitz is asked to go to the neighboring Mountain Kingdom with the objective of assassinating its prince, Rurisk. However, this is compromised when Regal reveals Fitz's secret mission to Rurisk's sister, Kettricken while drunk, rendering Fitz useless. Fitz finds himself in the middle of a plan to steal the throne for Prince Regal with the help of Galen, who tries to assassinate Verity, using the Skill. Prince Rurisk is poisoned and killed, leaving Kettricken, who is betrothed to Verity, the sole heir of the Mountain Kingdom. Fitz is poisoned and later submerged under water in a deep pool, a lazy attempt by Regal to finish Fitz off.
When Fitz feels he only has moments to live, he manages to contact Verity using the Skill to help him destroy Galen. He is rescued by his dog Nosy, who was not killed by Burrich, but sent to the Mountain Kingdom as a gift to Prince Rurisk. The rescue from the pool by Nosy left deep teeth marks in his hand that he comes to cherish as a sign of Nosy's love and loyalty. Nosy dies, being an old dog at this point— his true master, Rurisk is dead, and in the words of Fitz, Nosy "gave his life freely, remembering that we were good to one another when we were puppies." Fitz is healed by Jonqui, King Eyod's sister, afterward, and the last pages of the book tell how much Fitz laments the death of Nosy during that event and the pain of an older narrator at writing this.