The story begins with a young lieutenant junior grade Jacob Keyes and Dr. Halsey, they are going to a planet called "reach" where according to their studies a child with the perfect genetic composition of a soldier (one of about 300) lives, they arrive, and come to his school, and find him to be a boy named john wresting other boys off of a hill, completely unrivalled in strength.
Dr. Halsey kidnaps him and they take him away to a more interesting part of reach, the single largest military base controlled by mankind.
they rid him, and all of the other children of their last names, dubbing john to be john-117, the train the children by day and let them strengthen by night, teach them nothing but war strategy, by the age of 16 they decided the children were ready for body modifications, they coated their bones with titanium A, give them brain enhancing chips, sight sharpening surgery, and adrenal enhancements giving them unparalleled speed and reflexes. Along with several other strength and mind enhancing procedures, originally bred for crowd control, they would find greater use once the covenant appeared.
Through training, they were able to outsmart orbital drop shock troopers (like the ones from halo 2) and kill the best fighters on earth by age 10, but now, they were unstoppable.
After being put into use since the age of 18, the super soldiers were decorated like none other in combat (basically watch the movie "soldier". But their distinguishing moment was when the MJOLNIR battle suit was invented... the first volunteer was a marine, they let him wear the suit and he seemed fine, then they turned it on, the suit tightened, and because of the reflex machines inside exaggerating their movements, when he moved his arm slightly it completely shattered it’s entire skeletal structure. The resulting spasms of pain caused him to flail, completely shattering his entire bone system, and killing him.
Thus, the super soldiers the UNSC had created were the next up for this experiment, due to their bone augmentations, however, they could not only survive in this suit, but thrive, their reflexes doubled, their strength increased tenfold, they were near immortal.
John-117, having proven himself in combat the most distinguished, not for speed or strength, but for bravery and luck against dashing odds was pronounced the team leader for his selflessness for the sake of his team. (Oh, right... almost all of the super soldiers died in the augmentations).
One by one, his brothers and sisters were killed in combat once the covenant threat was seen, most of which died on the battle for reach, which ended with the covenant retreating and glassing (firing pure plasma at dirt turning it to glass) the planet.
After reach ended, began the war against the flood, which you can fill in as far as john-117 goes. After that came "The First Strike".
But, I’m tired of typing and you are probably tired of reading, so there's the origin of the master chief, anyway, and to find out the stories of EVERYONE ELSE check out the Halo book series.