The Emperor sends you to Morrowind to fulfill an ancient prophecy and become the reincarnation of a long-dead hero. The prophecies are incomplete and obscure, so to succeed, you must first find the missing clues. The prophecies also say to beware of a mysterious Morrowind cult called the Sixth House that worships Dagoth Ur, the immortal nemesis of Dunmer religion and an ancient enemy of Nerevar. You are therefore ordered to prepare yourself to face the threat of the Sixth House and Dagoth Ur.

The Emperor places you under the orders of the head of Imperial Intelligence in Vvardenfell, Caius Cosades, the Spymaster. Following the Emperor's orders, the Spymaster sends you to investigate the background and activities of the Cult of the Nerevarine and the Sixth House.

You learn that the Cult of the Nerevarine awaits a prophesied hero called the Incarnate, a reincarnation of the ancient Dunmer Hero Nerevar -- and evidence confirms the Emperor's belief that you may be the object of the prophecies. Also, the Sixth House and Dagoth Ur are the source of a supernatural blight that threatens to overwhelm the land of Morrowind and every living thing upon it.

Morrowind's most powerful religion, the Tribunal Temple, denies the prophecy of the Incarnate, persecuting the Cult of the Nerevarine as heretics. But you learn of a rebellious Temple faction called the Dissident Priests who may have the Lost Prophecies you seek. The Dissident Priests have also discovered that the Temple's immortal god-heroes -- Vivec, Almalexia, and Sotha Sil -- employ the same profane magics as Dagoth Ur, and that, grown weaker and weaker in their battles with Dagoth Ur, the Tribunal can no longer defend Morrowind from Dagoth Ur and the Blight. The Temple hierarchy, dominated by the Ordinators (the Temple's elite guard and inquisitors), will do anything to prevent the Dissident Priests from attacking the authority of the cult. By associating with the Dissident Priests, you becomes the target of Ordinator attacks.

As you dig deeper into the mysteries of the Nerevarine and the Sixth House, you are attacked by dark dreams, demented cultists, and fanatic assassins sent by Dagoth Ur and the Sixth House. When you finally locate and destroy a Sixth House base, you contract the terrible corprus disease, a supernatural weapon of Sixth House cultists. But when, with the help of an ageless Telvanni wizard, you are miraculously cured, that cure ironically fulfills one of the prophecies of the Nerevarine's reincarnation.

The recall of the Spymaster to the Imperial City leaves you without a patron and guide. You must thereafter rely on two native Dunmer for guidance: the Dissident Priest Mehra Milo, a friend and informant of the Spymaster, and Nibani Maesa, an Ashlander wise woman, seer, and leader of the Cult of the Incarnate. However, after you rescue Mehra Milo from the Ordinators who have imprisoned her in the Ministry of Truth, and receive from her the Lost Prophecies, you have everything you need to prove that you are indeed the prophesied Nerevarine.

To assume your identity as the prophesied Incarnate, you must provide proof to the Cult of the Nerevarine. First you deliver the Lost Prophecies recovered from the Dissident Priests to Nibani Maesa. Then you perform a quest for the Warrior-Protector of the Cult, Sul-Matuul, retrieving tokens from a subterranean Sixth House base.

A satisfied Sul-Matuul then reveals the secret location of the Cavern of the Incarnate, where you travel and encounter the Daedra Lord Azura, who confirms your status as the Incarnate, and gives you a token so that all Dunmer shall recognize you -- the Moon-and-Star Ring of Nerevar, an ancient magical treasure long believed lost, and known from legend to instantly kill any who wear it but Nerevar himself. Azura then interprets the Incarnate's prophecies, foretelling the next stages of the Incarnate's quest: to be acknowledged as war leader by each of the three Great Houses and by all four Ashlander tribes, and to reconcile the warring factions of the Tribunal Temple.

As described in the Lost Prophecies, the second stage of the Incarnate's main quest is to be named war leader of the four Ashlander tribes (the "Nerevarine") and war leader of the three Great Houses (the "Hortator"). When you have been named both Nerevarine and Hortator, you are invited to an interview with the Archcanon of the Tribunal Temple, Tholer Saryoni, and then with the God-Hero Lord Vivec. Vivec admits that he and the Tribunal have failed, and asks you to save Morrowind from Dagoth Ur.

The God-Hero Lord Vivec tells you that three great artifacts must be used to unmake Dagoth Ur and the Sixth House. Vivec gives you the first -- Wraithguard -- and tells you that the other two, Sunder and Keening, must be recovered from Sixth House citadels within Red Mountain's crater and defended by Dagoth Ur's lieutenants, the Ash Vampires. When you have all three artifacts, you must descend into Dagoth Ur's own citadel and use the artifacts to destroy the enchantments that give him his supernatural powers. With the enchantments destroyed, Dagoth Ur and all his minions are unmade, and the blight removed from Morrowind.