Reptile remains on the side he is on regarding the fate of Earthrealm humans for a simple reason: Raiden.
The Saurians, Reptile had been told, were driven from Earth because a massive battle between the Earth's protector, Raiden, and the Netherealm's god, Shinnok, had led to massive peripheral destruction of the Earth's environment and the Saurian civilization. He did not try to save places on Earth where Saurians lived; he instead focused his efforts on trying to stop Shinnok from taking over the actual planetary mass without regard to what was living there. Logic would dictate that Raiden was just as ruthless in protecting his realm as any of the other gods: it was not about the little creatures that lived there, it was about territory.
However, during the events of the first and second Mortal Kombat tournaments, it became clear to Reptile that Raiden was not who Reptile had believed him to be. Raiden was not only trying to save the realm itself - - like he had been when the Saurians had to flee - - but was also trying to save the humans who lived there. Raiden put every effort he could into preventing the Outworld war machine from coming to Earth and destroying the human species.
Ten million years ago, Raiden put no such effort into saving the lives of hundreds of millions of Saurians.
Yet, the Saurians were (or so Reptile had been told) a peaceful people, with respect for the environment of Earth, a sense of wonder at the minutest workings of nature, and reverence towards the magnificent and complex.
Society, as well, was magnificent and complex on Earth, obscured by hundreds of thousands of years of legend on the refuge of Zaterra. The Zaterran civilization never again reached the level of glory that the Saurian civilization had once achieved on their home planet of Earth.
The humans, however, were a new entrance to the world of higher sentience, and although their technology and their culture was growing at a rapid rate fueled by their short life spans, they took more than the Earth could give; took faster than the Earth could replenish. The Earthrealm was rapidly being destroyed by the humans.
Thousands of species of animals had gone extinct. Resources had been drained; ecosystems had been irrevocably changed. The humans were on a path to destroy themselves and their realm - Raiden's realm.
So why did Raiden try so hard to keep them alive? They were, after all, destroying his realm. Maybe it was because the humans looked so much like Raiden. Yet they knew not the protector of their realm. They believed in deities they themselves invented; deities who proclaimed that the humans ruled the earth and all shall bow down before them. Nature was to be conquered - such a wild-looking creature as Reptile could not possibly be as sophisticated as a human.
Yet Reptile and the Saurians had a 'human' form. Indeed, if they exhaled in the cold their breath could not be seen, but if Reptile walked among the Edenians, or the Outworlders, or any of the other humane-like species, not one of the mammals would run away in fear, or towards him in confused anger. Perhaps if they had all stayed in their human guises their entire lives, Raiden would have had empathy towards his race.
Reptile did not want Raiden's hypocrisy to save the race that was on the path to destroying the Saurians' original home, known only to Reptile in legend. Why did Raiden, a god, not see his own flaw? The Saurians had long lost faith in the gods; lost faith in the gods of earth. Zaterra had no godly protector when they fled there, yet Zaterra still had thunder, lightning, water, fire, earth, weather, animals, plants. . . the Zaterrans had no reason to believe that the gods were as powerful as they had once believed - just like the Zaterrans had no reason to believe that the gods were as righteous as the Saurians had once believed.
The Zaterrans had no guidance except that of the Matriarch, who, even without gods, was able to lead the Zaterrans towards restoration of Saurian civilization. It was a tiring, sobering, and desperate path to travel, one that creatures with souls should never have had to experience: The collapse of an ancient civilization in an instant - - and the godless task of rebuilding millions of years of culture, history, architecture, science, tradition - in one generation.
Time had passed. The Zaterrans were becoming proud again, no longer Saurian refugees but a culture of their own. They were nowhere near the glory of the fallen Saurian empire, but it would come with time.
That time never came. The Zaterrans, who, for generations, had been focused on rebuilding their world on a new planet, had hardly put any effort into their military. There was no one else on the planet of Zaterra to fight them, and the Saurian tradition of martial arts was not forgotten; it had evolved even further as Zaterran crab and Kirehashi. The oldest form would be found by human monks on an ancient mural in what they called Southern China, displaying forms and fights - and the humans would call this martial art Hung Gar, where it was then on known as one of the five Shaolin families of Kung Fu. Humans mistakenly called Hung Gar the Tiger-Crane style, for they believed Tigers and Cranes to have existed when the art was developed. The Five Elements Fist and the Iron Thread Fist were the closest to the Saurian art, for the Shaolin who had discovered the records of the Matriarch must have realized the wisdom of the Saurians, garnered over millions of years of experience: trials, errors, triumphs, defeats, advances, regressions, wars, times of peace. But no creature could combat the power of the gods - much like no human alone could fight against a bomb falling from the sky.
Thus, the Zaterrans had no enemies to toughen them, and no gods to protect them. It was the Matriarch alone who the Zaterrans had to protect them from Onaga's conquest of Zaterra.
The same fate that had befallen the Saurian civilization on Earth had befallen the Zaterran civilization in its infancy. The Zaterrans fought valiantly; their ancient martial arts and weapons did not fail to destroy the enemy. Yet, no matter how many enemies they killed, the corpses would simply stand up and fight again. No mortal can fight a tireless enemy and succeed. The Zaterran civilization collapsed of mere exhaustion.
And so Zaterra merged with the realm of Outworld. Taken from one part of the universe to another, yet without disrupting the fragmented universe as a whole, one planet - Outworld - grew in size as it encompassed worlds. The environment of Zaterra would change as the planet was somehow flattened like a ball of clay to make up a patch of Outworld. Places would freeze in Zaterra, other places would dry out. Not many of the indigenous creatures would survive, and the adaptable Zaterrans themselves were hunted out and killed.
Reptile was born in this mangled realm of Outworld, child of a remote village still hiding in the mangled patch of Zaterran land, where few Raptors managed to survive. But they, too, were found, and they were enslaved, like every other sentient being forced to live on Outworld. He was to be the guard of the wizard who ate human souls. He was to serve the successor to Onaga, the tyrant who, before Reptile was born, had destroyed his race's world and attempted to exterminate not only the Zaterrans themselves, but any trace of their civilization.
Reptile was even given the promise that his service would lead to the emancipation of his race. Perhaps they could again find a new home to live in peace.
Thousands of years had passed and Reptile realized that his race would never be free unless he took action.
At the Outworld Mortal Kombat tournament, Reptile valiantly attempted to kill Shang Tsung to send a message to the Outworld emperor - - to make good on his promise.
He failed.
Shao Kahn killed them all.
And Reptile remained, nowhere he could go, nothing he could do to reverse the extinction.
Saurians - - Zaterrans - - Raptors - - whatever they might be called - - Reptile's kind had not been stupid. Reptile knew that, by the time he was born, the Saurians were a race that was functionally extinct. There were not enough Raptors to sustain the species for much longer than a few more generations until all of the Raptors were related, at which point they would not marry their cousins. The Zaterrans were doomed before Reptile was born, so the destruction of his people was not truly Reptile's fault.
It took very little cognition to link the inevitability of the Saurians' demise with the battle on Earth between Raiden and Shinnok. Forced to abandon countless years of civilization for a clean slate in a new, foreign, unfamiliar home, without a god's help, without a god's protection - - how could anyone be expected to survive?
Raiden, an eternal god, must have seen this coming. At the time, Raiden might have succeeded in protecting Earth, but he failed to protect the Saurians' home.
Now, Raiden had put his efforts into protecting the humans' home, at the expense of Earth.
Reptile could not side with the humans, despite the genocide of his people at the hands of the Outworld.
Reptile blamed himself for the final blow struck at his race, but he was not the one who had sealed their fate.
Raiden had doomed the Saurians, and Reptile would make sure that Raiden doomed the humans as well.