For 2500 years, Sauron ruled Mordor uninterrupted. Having wrought the Ring, it was from there that he launched the attack upon the Elves of Eregion. He was repelled by the Men of Númenor. Almost a thousand years later he fought the Númenóreans again; this time, he was captured by the Númenóreans and brought to their island kingdom, eventually causing its destruction (see Akallabêth). Immediately after Númenor's destruction, Sauron returned to Mordor as a spirit (the last of his living being having been bound to the One Ring) and resumed his rule.

Sauron's rule was interrupted yet again when his efforts to overthrow the surviving Men of Númenor and the Elves failed, and they formed a Last Alliance of Elves and Men whose army advanced on Sauron's land. A great battle took place on the Dagorlad in which Sauron's forces were destroyed and the Black Gate was stormed. The Barad-dûr was then besieged by the Alliance's forces. After seven years of siege, Sauron broke out and was defeated in a final battle on the slopes of Orodruin. After his defeat the Barad-dûr was levelled and great fortresses were built at the entrances to Mordor to prevent Sauron's return. For over a thousand years, Mordor was guarded by Gondor and remained desolate, although the watch was lessened somewhat during the reigns of some of the Kings.

Casualties from the Great Plague, during the reign of King Telemnar, were so high that the fortifications guarding Mordor were abandoned as the troops were called back to Gondor's cities. As the guard slackened, Mordor began to fill with evil things again. The Ringwraiths took advantage of Gondor's defeat in TA 1856 to reenter Mordor and the final fortresses held by Gondor were abandoned and fell into ruin sometime after TA 1944. In 2002 Minas Ithil was conquered by the Nine Ringwraiths; and the fortifications that were supposed to defend Gondor from the menace inside Mordor were turned into a means of shielding Mordor. By the time Sauron returned into Mordor after his false defeat in Dol Guldur (in the events that took place at the time of Bilbo Baggins's quest), Mordor was protected too well to be captured by any military might that was available in Middle-earth at the end of the Third Age. In the north of Mordor during the War of the Ring were the great garrisons and forges of war, while surrounding the bitter inland Sea of Núrnen to the south lay the vast fields tended for the provision of the armies by hordes of slaves brought in from lands to the east and south.

During the War of the Ring, Sauron gathered all his forces to Mordor. After the Battle of the Pelennor Fields, a Host of the West went to the Black Gate. Sauron sent his army to destroy the Men of Gondor and Rohan, but then Frodo Baggins destroyed the One Ring and Mordor fell. The Dark Tower, the Black Gate and the Towers of the Teeth were destroyed. Mount Doom exploded, clearing the sky over Mordor. Both Sauron and his Ringwraiths were apparently destroyed.

After the ultimate defeat of Sauron, Mordor became mostly empty again as the Orcs inside it fled or were killed. Crippled by thousands of years of abuse and neglect, but capable of sustaining life, the land of Núrn was given to Sauron's freed slaves. Gorgoroth remained desolate in the early part of the Fourth Age.

The armies of Mordor bore upon their armor and shields the red Eye of Sauron on a black field. This was also flown on the banner that accompanied the Lieutenant of the Tower of Barad-dûr when he confronted the emissaries of Gondor.

At the time of the War of the Ring, Sauron had gathered great armies to serve him. These included enslaved Men of the East and the South, who spoke a variety of tongues, and Orcs and Trolls, who usually spoke a debased form of the Common Speech. But within Barad-dûr and among the captains of Mordor (the Ringwraiths and other high-ranking servants such as the Mouth of Sauron), the Black Speech was still used, the language devised by Sauron during the Dark Years of the Second Age. In addition to ordinary Orcs and Trolls, Sauron had bred a stronger strain of Orcs, the Uruk-hai, and very large Trolls known as Olog-hai who could endure the sun. The Olog-hai knew only the Black Speech.

Mordor actually has two meanings: "Black Land" in Sindarin, and "Land of Shadow" in Quenya. The root mor ("dark", "black") also appears in Moria, which means "Black Pit". Dor ("land") also appears in Gondor ("stone-land"), Eriador, and Doriath ("fenced land"). The Quenya word for Shadow is "mordo".

A proposed etymology out of the context of Middle-earth is Old English morðor, which means "mortal sin" or "murder". (The latter meaning is descended from the former.) It is not uncommon for names in Tolkien's fiction to have relevant meanings in several languages, both languages invented by Tolkien, and actual historical languages. Tolkien was a professor of Anglo-Saxon, so his word roots tend to be Anglo-Saxon/Nordic/Germanic. Mordor is also a name cited in some Nordic mythologies referring to a land where its citizens practice evil without knowing it, imposed on themselves by the society long created for that purpose.[citation needed] This quite fits with Tolkien's Mordor.