The primary indigenous sentient life form living on Earth are humans. According to Rock of Ages, what is not generally known in-universe is that humans also lived hundreds of millions of years in the past, when the planet's continents were joined as the supercontinent Pangaea. Then, too, humans developed into an advanced global civilization. But they severely abused the planet and its resources, eventually destroying their own civilization and virtually all their own species in the Permian–Triassic extinction event. In a last ditch effort to save the human race, they sent transport pods across deep space containing pairs of a human male and human female in stasis in the hopes that they could multiply and replenish their species on other worlds. (This may or may not include D'Hoonnib, an alien planet populated by Federation humans that developed in ignorance of the Earth's existence.) Some of those pods never left Earth, and would reawaken from stasis on the planet hundreds of millions of years later.
Superficially, the "modern" Earth of the Mirage TMNT universe has an in-universe publicly documented history much like that of the real Earth. There are supernatural elements including the parallel world of Nocturna, the Time Scepter, the Warp Crystal, as well as Lovecraftian gods like Karenthog Sar Routolo, but these all remain secret or occult. There are also superheroes like the Justice Force who varyingly maintain a public presence such that they are not considered fictional in-universe. Additionally, this version of Earth has also been secretly visited by technologically-advanced aliens including the Utroms, whose accidental spill of mutagenic transport fuel made possible the mutations of Hamato Splinter, his four turtle sons and Leatherhead.
According to volume 4, in 2002, the Utroms finally make official public first contact with the Earth, offering new opportunities for technological and cultural exchange, and global society rapidly changes within the space of six months. After this, the Earth becomes populated by all manner of alien immigrant residents who travel through the Utroms' new Transmat facility near New York City. The Utroms do not reveal the truth of their secret past visits or their involvement in the T.C.R.I. incident, and as such they also ask the six Earth mutants to help them keep their secret; this allows those mutants to finally live public lives, but they must still "hide in plain sight" by identifying themselves as "aliens."
According to Dark Shadows, several years later, the Utroms reveal that the real reason they visited the Earth was that their scientists could detect an imminent planetary cataclysm that would drastically tilt the Earth's axis and destabilize its tectonic plates. With this revelation, the Utroms offer to evacuate all the humans who wish to leave, and the vast majority of the planet's population takes up the offer. A much smaller population of humans is left behind, and not only do they prove inadequate to continue maintaining Earth civilization as it had been, but they are largely helpless to fend off the effects of catastrophic global warming that flood the planet's low-lying areas including the ruined former New York City, as seen in Day in the Life.
According to Swan Song, by the late 21st century, Earth civilization's fortunes appear to be reversing, and great cities have been rebuilt or rejuvenated and appear to thrive again including Dubai, Hong Kong, London, Montreal, New York City, Paris, San Francisco and Sydney. According to Silent Night, Tōkyō also appears to have recovered. Just as before the cataclysm, the Earth's population still includes a large population of resident aliens.