The Utroms have been at war with the Triceratons on and off, and have are in another engagement. Seeking warriors strong enough to combat them, they go to Earth where they can research safely and make new warriors out of some of Earth's animals most similar to the Triceratons.
Splinter is Specimen 0 as a test subject, and he is entrusted to the care of the Utrom Guardian Hamato Yoshi of the Foot Clan, as well as his wife Tang Shen, the scientist giving him mutagenic injections.
The testing goes surprisingly well; Splinter learned martial arts at the same time as the injections, and was able to show combative prowess before he developed the ability to speak.
Soon, General Krang of the Utroms decides he's had enough with "playing around with rodents" and demands actual warriors. Conveniently, Splinter is practically human mentally and so full of admiration for Yoshi and Shen that he wants his own students to honor them.
They almost go for an albino alligator that the Utrom scientists found in the sewers, but when it's mutated, it imprints on the scientist that found it. So, Hamato Yoshi brought Splinter four turtles instead.
In three years, the turtles were mutated to bipedal and speech capacity, and Splinter's mental development was nearly complete.
Oroku Saki comes around and gets into a fight with Yoshi, which results in a fire. Splinter flees with into the sewers with the turtles, as they were nearest to him, and returns in hopes of saving Yoshi and his family, but arrived too late. The home was gone, and he saw the Utroms investigating the damage.
This is where I think I get a little sloppy, since instead of going to the Utroms for help, he decides to strike out on his own with his turtles.
Which of course makes Krang unhappy, as the blueprints for his soldiers have gone missing. And of course, he takes his anger out on Saki, whose temper resulted in years of research disappearing in a puff of smoke.
There is one situation that is worse than the Triceratons and the Utroms being at war with each other, and is even a result of their war.
The Triceratons and Utroms abandoned a planet they had been warring over, leaving room for a new Malignoid Queen to establish her hive. Over the years,
the Malignoids restored the planet to its former glory, except for one problem:
the war caused an environment for a
cordyceps-like fungus to flourish and begin to infect Malignoid drones. At first, the planet was contained to prevent the infected Malignoids from escaping, but now those efforts are beginning to wither.
All the while, the turtles know nothing of their origins, nothing of the Utroms.
Only that their Master Splinter's beloved parents was murdered by 'the Shredder' - or so he believed.
(Also, 'the Shredder' isn't Saki's official codename, it's just what Splinter thought of Saki as because of his armor.)