This novel begins directly where its predecessor, The Fellowship of the Ring, left off. Aragorn searches for Frodo Baggins, the hobbit in charge of carrying the One ring into Mordor. Frodo and Sam, his servant, have left the others after their companion Boromir tried to steal the ring. Orcs attack the remaining members of the fellowship.
Boromir, no longer under the ring's influence, fights to the death to protect Merry and Pippin, who are also hobbits, but the Orcs take them captive. Aragorn finds Boromir as he lies dying. The latter confesses to how he tried to take the ring. He admits that Aragorn is the braver man and the rightful heir to the throne of men. Gimli (a dwarf) and Legolas (an elf) arrive to see Aragorn mourning Boromir's death.
After arraying Boromir's body for burial and setting it to float down the river toward his home in Gondor, the three friends decide not to follow Frodo. They believe the hobbit has a better chance at traveling undetected without them. Instead, they seek to save Merry and Pippin from the Orcs. The enemy is traveling quickly, running even during daylight, which is against their nature.
Merry and Pippin realize the Orcs think they [the hobbits] are valuable to Sauron. When a fight breaks out between the Orcs following Sauron and those loyal to Saruman, Pippin cuts the ropes that bind his hands but pretends to be bound. Later, Saruman's Orcs take Pippin and Merry and try to outrun the others. The Orcs are overtaken by the Riders of Rohan. During the battle, Merry and Pippin escape into Fangorn Forest.
Aragorn finds hobbit prints in the dirt along with the elfin brooch from one of their cloaks. The friends rejoice that at least one of the hobbits is still alive. The following day, they meet the Riders of Rohan, who are skilled horseman and soldiers. Éomer, their leader, explains that they attacked a group of Orcs the night before and killed them. Aragorn asks if they saw any hobbits among the dead. Unfamiliar with that diminutive species, Éomer assures them that they left none alive. He gives Aragorn and the others two horses to use in their search. Then he warns them that Saruman, a former good wizard, is amassing an army in his fortress to fight for Sauron.
Aragorn tells Éomer that Gandalf the Grey was killed. That night, Aragorn, Legolas and Gimli find the remains of the Orcs but no signs of the hobbits. While they sleep, Gimli believes he has a vision of Saruman by their camp. In the morning, their horses are gone.
Meanwhile, the hobbits meet Fangorn, known as Treebeard. He is an Ent, a tree-like creature that can walk and speak. Fangorn brings the hobbits to his home where he gives them Ent-wash, a nourishing liquid, to drink. The following morning Fangorn brings them to the Entmoot, a gathering of the remaining Ents. They will decide whether to go to war against Saruman and his forces at Isengard. The Ents are rallied to fight. To Pippin's eyes, it seems the entire forest begins to march to Isengard.
Aragorn, Gimli and Legolas find clues that the hobbits have escaped. They follow the trail into Fangorn Forest but are surprised by an old man in a Grey cloak. Fearing it to be Saruman, they draw their weapons. The old man leaps to a rock and throws off his cloak, and they eventually recognize their old friend and leader, Gandalf.
Gandalf explains that he is now Gandalf the White, having passed through fire and survived. He further explains that Saruman's forces are marching against the men of Rohan, but that he's kept some of his soldiers away to protect Isengard. Meanwhile, Sauron has sent his armies out against the kingdoms of men, and to search for the One ring. There is hope that Frodo will be able to sneak through the weakened guard in Mordor. Gandalf has their horses and gives the horses to them. He calls Shadowfax, the fastest horse in the world, for himself, so they can travel together.
When they reach Édoras, or the Golden Hall, they are instructed to leave their weapons outside by order of Gríma Wormtongue, the king's counselor. Gandalf insists they be allowed to see King Théoden and that he be allowed to keep his staff as a walking cane. The guard finally agrees, and they approach the king. Gríma insults Gandalf, but the wizard soon calls down thunder with his staff, forcing Gríma to the floor. Théoden rises and walks out of the hall into the sunlight. The fresh air seems to return him to his senses. He forces Gríma to choose between fighting with Rohan against Saruman's army or fleeing to Isengard. Gríma flees.
The king then gives armor and weapons to Aragorn, Gimli and Legolas. Gandalf takes none, but asks for the horse Shadowfax, which had only been loaned to him before. Théoden agrees. As the king and his men prepare to leave, he calls for a man to stay behind and act as leader for the people left in Rohan. His counselor suggests that Éowyn, Éomer's sister and the king's niece, be given the reins of leadership.
As Théoden and the others travel to Helm's Deep — a great fortress of Rohan — Gandalf suddenly declares he must leave the group. The others proceed to Helm's Deep and fight Saruman's armies from there. The Orcs attack the fortress the following day and nearly overtake the forces of Rohan. Théoden rallies Aragorn and the others to ride out with him in full armor as a last attack against the enemy. Their bravery and power throws the Orcs into confusion. Gandalf arrives with reinforcements, and Saruman's armies flee.
Once the battle is over, Gandalf tells the king to gather a small guard to accompany him to Isengard. They must speak with Saruman. Théoden chooses Éomer and 20 others while Aragorn, Gimli and Legolas continue to accompany Gandalf. Gandalf and his friends are delighted when they are welcomed to Isengard by Merry and Pippin. The hobbits lounge by the gate of the stronghold, smoking their pipes and drinking ale. While Gandalf and the king seek to talk to Fangorn, Merry and Pippin bring the others to Saruman's storehouse where they find food and tobacco. The hobbits tell their friends about their adventures and how the Ents defeated Saruman.
The group calls on Saruman to speak to them. When the wizard does appear, he tries to use his power to bewitch those listening into following him. Gimli rebukes the wizard, and Saruman loses his hold over the others' minds. Gandalf breaks Saruman's staff, effectively causing the wizard to lose his power. Gríma throws a crystal sphere at Gandalf, but it misses. Pippin picks it up. Gandalf asks Fangorn to release the dam and flood Isengard so that Saruman cannot escape. Gandalf takes the crystal from Pippin, and the company leaves Isengard.
That night, consumed with thoughts of the crystal, Pippin creeps from his bed and steals the sphere from Gandalf. As he studies the crystal, he sees a dark, winged creature seeking him. Then Sauron himself questions Pippin, at first believing him to be Saruman. When Sauron discovers it is a hobbit holding the crystal, he demands that Saruman not keep the "dainty" for himself; he will come and retrieve it. Pippin screams and releases the ball.
The scream alerts the others and they rush to Pippin's side. The hobbit admits his folly. After examining Pippin's mind, Gandalf is convinced that Sauron is still unaware of Frodo's quest. In fact, Sauron will be following Pippin, believing him to have the ring. Gandalf takes Pippin on Shadowfax, and the two head back to Édoras.
Meanwhile, Frodo and Sam struggle to find a way down the mountains and to the gates of Mordor. After days of wandering, they seem no closer. Their food is getting scarce, with only a few squares of elvin lembas bread to eat. Gollum, the creature who used to own the One ring, sneaks into their camp, hoping to steal it from Frodo. The hobbits take the creature captive. He promises by "the precious" to show them the way to Mordor. The three travel through the Dead Marshes, a place haunted by the spirits of fallen warriors of a great battle between men, elves and Orcs.
One night, a nazgúl flies overhead. The creature obeys Sauron and searches for the ring. Frodo overhears Gollum arguing with himself about obeying the hobbits. He swears he will protect the precious and do all he can to keep it from the Dark Lord. It is evident that Gollum doesn't like Sam and only obeys Frodo because he has the ring. Gollum leads them to the gates of Mordor but prevents Frodo from entering. He says there is a hidden path into Mordor that Sauron has forgotten.
As they travel to the new path, the land becomes less desolate. Sam sends Gollum out to find something to eat rather than lembas bread, and the creature returns with several rabbits. Gollum is appalled that Sam wants to cook them and warns that a fire may alert their enemies to their whereabouts. The hobbit sends Gollum out to find some herbs so he can make a stew for Frodo. The fire draws the men of Gondor to their camp.
Their leader, Faramir, is intrigued to learn that the hobbits were once in the company of his brother, Boromir, son of the High Warden of Gondor. Frodo explains that they were all involved in a quest foretold in an ancient song. Faramir is familiar with the song and asks Frodo if he knows what Isildur's Bane is, but the hobbit feigns ignorance. (Isildur's Bane is the One ring.) Faramir must leave Frodo and Sam in the care of two of his soldiers as enemies approach. The men of Gondor fight a battle with a small army of Sauron's men, after which, they force the hobbits to accompany them back to Minas Tirath, the capital of Gondor.
Faramir repeatedly questions Frodo about his relationship to Boromir. Faramir also explains that Boromir's horn, which he would never abandon, was severed into pieces that floated to shore along a river. Faramir knows his brother is dead and believes Frodo knows how it happened. The hobbit finally convinces the man that Boromir was alive when last he saw him. Sam accidently spills the fact that Boromir tried to steal the One ring from Frodo. Faramir is saddened that his brother could not fight against its power and vows he won't try and take it from Frodo.
Gollum is captured by the soldiers and taken prisoner. After interrogating the creature, Faramir tries to convince Frodo not to trust Gollum. He also warns of a hidden danger along the path Gollum wants them to take to Mordor. Frodo insists he and Gollum are bound in this quest. Eventually Faramir sends them on their way with fresh supplies and his hope they will one day meet again so he can learn the whole of Frodo's story.
Gollum leads Frodo and Sam up a steep mountain and into a dark tunnel. The creature then abandons them in the blackness. The hobbits struggle to find their way but are soon overwhelmed by an intense feeling of danger. Sam reminds Frodo of the phial of Galadriel, a gift the elfin queen promised would give them light. Frodo raises the phial, and Shelob is revealed. The giant spider hungers for fresh meat but turns away when confronted with the light of Galadriel and the threat of Frodo's sword, Sting. The hobbits flee toward the exit but before they can escape, Shelob sneaks between them. Gollum holds Sam back as the spider poisons Frodo. Sam manages to escape from Gollum.
Fueled by his grief, Sam takes Frodo's sword and kills Shelob. Fearing approaching Orcs, Sam removes the ring from Frodo's body and puts it on. He finds he can see in the dark and understand the strange language of the Orcs. They laugh that Frodo is in for a surprise when he wakes up later. Sam is angry with himself for assuming his friend was dead and not just stunned. The Orcs wonder at the mighty warrior that harmed Shelob and who must still be in the tunnels.
Sam follows the Orcs, who talk about bringing the prisoner to their superior to be searched and questioned. Sam draws Sting and tries to divert their attention, but no one pays him any mind. They bring Frodo into a tower and lock the door behind them, leaving Sam alone.