The Y'Lyntians (often incorrectly called Atlanteans) are a dying people who once ruled the Earth ten thousand years ago with the aid of the sun crystals and serve as the basis for the myth of Atlantis.
Many millennia ago, the Y'Lyntians were simple inhabitants of the island of Y'Lyntias, until it was stricken by a shower of large, mysterious crystals raining from outer space onto their island. The largest one, known as the Sun Crystal, landed on top of the high mountain. Then, the planets aligned, imbuing the crystals with a powerful energy which the Y'Lyntians learned how to harness. Using these objects, the Y'Lyntians advanced their civilization far beyond any other allowing them to build a utopia for themselves.
However, this paradise had its dark side: believing themselves superior to all others, the Y'Lyntians began enslaving human beings in order to do physical work. As the new workers could not perform all necessary tasks, those who unfortunately could not work well were eventually transformed by the Crystal Sun into a series of mutants; either the Beast-people for heavy physical labor; the Merpeople to hunt in the sea for food; and Avians to patrol the skies, preventing certain Atlanteans from escaping and were kept in a cage so as to not foul purity. A number of Y'Lyntians opposed the dark ways of their own people but they were in the minority and were never successful in overthrowing them, their opinion was brutally suppressed as soon as it was out in the open.
But finally, the human cultures had enough and banded together to destroy the tyranny of Atlantis. The Y'Lyntians used their sun crystal to annihilate the human fleets. But many of the mutant slaves were allied with the human forces and redirected the Sun Crystal's own energies back at it destroying it, and sinking the island of Atlantis to the bottom of the sea. Over the following centuries and millennia, the name is slightly distorted until the legend of Atlantis was born.
A few Y'Lyntians managed to escape the destruction of their homeland with a significant fragment of the Sun Crystal and came to America and hid underground, in order to protect themselves from the wrath of the rest of mankind, where they constructed a new city in a huge cavern beneath New York, powered by the energy of the fragment that became known as the Crystal Moon. Keeping watch over the world's progress, the Y'Lyntians established an outpost directly under the place where New York City was later built to observe everything, one fateful day, it became the new hiding place of the Ninja Turtles and their master Splinter.
But the New York Group of Y'Lyntians came after some time into great distress, as the Crystal Moon was running out of power and without slaves the Y'Lyntians could not survive on their own. Only a certain planetary alignment would allow them to gain new energy. Almost the entire populace went into crystal suspension to wait for the next alignment to recharge the crystal. Only one remained awake, the High Mage or the Entity, whose job was to watch over the city until the Crystal Moon could be recharged.
After centuries The Entity also watched the Foot Clan's efforts in attempt to locate the Utroms underground base and mutated innocent humans in an underground Foot laboratory to achieve that end. He lured the mutants, as well as the Turtles, when they wanted to investigate the mystery of the horde of mutated humans, to his city, claiming they could have a new home and to repopulate the city. He soon turned violent, and got into a fight with the Turtles, but ended up in suspension like the others.
When the next planetary alignment recharged the Sun Crystal, the Y'Lyntians reawakened, planning to reaffirm their rule over the Earth. Using the Crystal Moon, they attempted to rise their ancient city Atlantis from its watery grave to the surface again, which would cause a mass geological variation on Earth, wiping out most of civilization. A moderate Y'Lyntian, Versallia, helped the Turtles to defeat these selfish plan. They were stopped when the Turtles took a page from history and redirected the energies at the Crystal Moon, the New York colony and nearly all of its inhabitants were then destroyed as lava consumed the entire city.