The lion turtle is one of Avatar: The Last Airbender's most fascinating magical creatures, thanks to the mystery of its past. The show features many amazing and magical animals, also including air bison, winged lemurs, and dragons, and the lion turtle, who shows up in the Avatar finale to help Aang holds a special place. Only one lion turtle is present in Avatar: The Last Airbender, even though many existed thousands of years before the events of the series. So what happened to them?
In The Legend of Korra, viewers encounter Wan, the first ever Avatar, and experience the early world of the Avatar universe. When Wan was alive, humans lived in cities on the backs of giant lion turtles like the one who appears in Avatar: The Last Airbender. The lion turtles protected the humans and also provided them with the means to protect themselves: whenever humans had to venture into the spirit wilds beyond their cities, the lion turtles gave them the ability to bend one of the four elements through energybending.
Different lion turtle cities gave different elements to their inhabitants. Wan's original city was atop a lion turtle who gave people the power to control fire. As Wan traveled the world, he encountered lion turtles with an affinity for air, water, and earth. This proves that there were at least four lion turtle cities in the world, although it's likely there could have been more - the exact amount of lion turtle cities is never specified. However, lion turtles seem to have passed out of common knowledge by the time Aang becomes Avatar. The lion turtle who teaches him energybending is the only one to appear in the series, meaning that something must have happened to the rest of the lion turtles.
According to Nickelodeon, the lion turtles were hunted to near extinction during the ten thousand years between Wan's time as the Avatar and The Legend of Korra. Even though they are the largest beings in the Avatar universe and possess the powers of the elements, lion turtles come across as fairly peaceful and isolationist, so it's unlikely they fought back or banded together as they were being hunted. Just how the humans managed to kill these city-sized creatures with limited technology has not been clarified, but what is clear is that Aang's lion turtle is the last one left. He disguised himself as a floating island and made sure to stay far away from any humans who may harm him.
Unfortunately, the lion turtles are not the only species hunted until they were nearly extinct features in Avatar. In season 3, episode 13, "The Firebending Masters," viewers learn of the Fire Nation's complicated past hunting dragons. While Sozin was Fire Lord, he began the tradition of hunting dragons for sport - anyone who killed a dragon would earn the title of 'Dragon' themselves. Iroh claimed to have killed the last dragon, but in reality, he had lied to protect the last living dragons, Ran and Shaw. In Legend of Korra, Zuko flies on Ran and Shaw's descendant, a dragon named Druk.
Despite being large and powerful beings, the lion turtles, like the dragons, were hunted almost to extinction. That is very much proof of humans' capacity for cruelty throughout Avatar: The Last Airbender, reaffirming the need for an Avatar who can keep balance and protect the world. Still, it is good that Aang's lion turtle survived for as long as he did, as he helped Aang when he was in need and deepened the lore of Avatar: The Last Airbender.