The first level, the Slopes of Mt. Doom, sets the player in the final battle of the Siege of Barad-dûr. Isildur does battle with many orcs and after the level is completed, a cutscene shows how he defeats Sauron (though he does not truly perish) and takes the One Ring. Isildur is influenced by the Ring and refuses to destroy it when he has the chance. This is really a training level. Next, Aragorn and the hobbits approach Weathertop, a hill about midway between the Shire and Rivendell. They camp on the hill, but are attacked in the night by the Ringwraiths. Aragorn successfully drives them off, but not before Frodo is stabbed with a Morgul-blade.

After reluctantly agreeing to detour through Moria to continue the Quest of the Ring, the Fellowship travel to the Gates of Moria. Traveling through snow, rocky terrains and eventually marshy grounds, the companions make it to the Doors of Durin, but are soon attacked by the Watcher. After slaying the creature they continue into Moria. In a chamber in Moria, the Fellowship finds Balin's tomb. Soon after entering orcs can be heard rallying towards the room. After holding their ground and slaying many orcs, a cave troll arrives, but the collective efforts of the team defeat it; Frodo is speared in the chest by the troll, but he is saved by his mithril coat. The nine companions manage to get to the exit, but on their way to the Bridge of Khazad-dûm they are confronted by Durin's Bane, and Gandalf sacrifices himself to allow the others to get out of Moria.

The Company of the Ring pass by Amon Hen and are ambushed by a large party of Uruk-hai—a stronger, faster breed of orcs that can travel without hindrance in sunlight. The Fellowship is broken up during this battle, with Aragorn, Legolas and Gimli slaying as many of the enemy as they can, and Boromir being left alone to defend the hobbits. Sam and Frodo escape, Merry and Pippin being captured by the Uruk-hai, while Boromir is overwhelmed by their sheer numbers. He is slain by Lurtz, the leader of the Uruk company, before Aragorn, Legolas and Gimli can reach him. After avenging their comrade's death, the three set out to find Merry and Pippin. Aragorn uses his skills of tracking to trace the Uruk-hai that captured Merry and Pippin to Fangorn Forest. Deep in the forest they encounter a white wizard. At first they believe it to be Saruman before realising that it is Gandalf, who they thought had been killed in Moria.

Meanwhile, Saruman's legions of Uruk-hai and Orcs ravage the countryside of Rohan virtually unchecked, burning and killing at will. Saruman has provided his evil forces with an explosive mixture, which, when lighted, causes massive damage. Uruk-hai Berzerker Bombers, some suicidal individuals with this concoction strapped on their back, join the army rushing through Rohan destroying towns and villages. Aragorn and the Rohirrim must stop this destruction and save the villages of the Westfold. Saruman sends more of his forces to crush the resistance of Aragorn, Legolas, Gimli, and Gandalf at the gap of Rohan. This time, the armies include wargs. Along with their riders, wargs are extreemely difficult to kill without sustaining a great deal of damage.

Aragorn, Legolas,and Gimli manage to survive all this and join the remaining forces of Rohan at Helm's Deep for the Battle of the Hornburg further aided by the Lórien Elves led by Haldir and sent by Elrond. They are able to hold off the Uruk-hai but the attackers blast a wide hole in the wall using the explosive devices invented by Saruman, a "blasting-fire". After the wall is breached, hundreds of Uruk-hai and other orcs flood inside the walls of the fortress. After sending the women and children deeper inside, one of the three main heroes is tasked with defending the door to the inside. Defeating many enemies and even disabling a dangerous catapult, he succeeds in defending the door. It is revealed that the door to the Great Hall is being assaulted as well. After battling and nearly managing to repulse the attack of multiple Uruk-hai warriors, common orcs and archers, two cave trolls are sent in to destroy the door once and for all. But this last ditched attempt to win the battle fails. Gandalf comes with Éomer and his men and save the day. The end of the battle of the Hornburg is also in the start of The Return of the King video game.

Tower of Orthanc is a bonus level, not relevant to the story, in which Saruman gathers all the forces that remains under his command and unleashes them upon the player as they climb the 20 levels of Orthanc. After the player fights through many orcs, Uruks and Trolls he confronts Saruman. But the rogue wizard uses his magic to teleport and escape, leaving the player stranded at the top of Orthanc. Once you complete this level with any character, you will unlock Isildur at level 10