Oh sure, the in-universe explanation is that the fallen Valar Melkor, who became known as Morgoth the Black after his destruction of the Trees of the Valar, used his might to pervert and destroy the works of the other 11/12 Valar and "brought forth fire and leveled mountains and raised valleys" to create hellscapes out of their work, such that the Earth, instead of a garden, became discordant and all the plans of the Valar were marred. After the end of the First Age, when the host of the Valar came to the aid of Middle Earth and destroyed Melkor's fortress, and brought him to judgement to be cast into the Outer Dark, there was further geologic destruction as the powers of the hosts basically destroyed the continent/region of Middle Earth known as Beleriand.

After THAT there was a further catastrophe as the Numenoreans, corrupted into the Dark Arts by Sauron, who was their captive, decided to wage war on the Valar, who they believed were keeping the secret of immortality from them. The Valar were in a pickle, and abdicated their powers and called on Eru to judge, because this was outside their mandate. He Atlantis'd Numenor and destroyed the majority of their people (who had turned to worshiping Morgoth) - the Numenoreans who founded Gondor and Arnor and who created the political landscape of the Third and Fourth Ages were the remnant of that fallen civilization, who were warned of the destruction of the isle of Numenor and escaped on boats.

Also it can be supposed that Mordor was a partial creation of Sauron, who fled there after the fall of Numenor as a spirit (could be wrong about that)