A History Lesson

Alright Emo dawg, this is for you. Ted says to give a brief summery so here goes.

Ok so you have a the Covenant. They're a conglomeration of alien races with a strict hierarchical theocratic society, with each race holding some level of power over the others (or at least being roughly equal to them in some instances) and with (of the known races) the Prophets at the top and the Grunts at the bottom.

The Prophets evolved into sentience on a world which was a former outpost of the Forerunners and on which much of the Forerunners technology survived intact. They considered the Forerunners to be gods and their technology to be divine gifts by these gods and so developed a religion based on them. The first other species they ran into were the Sangheli (Elites) who evolved on another former outpost world but saw the Forerunner relics as sacred things left by the gods that should not be meddled with. This difference in ideology led to war between the two species and after almost being wiped out by the prophets with their advanced Forerunner technology, they finally submitted and thus was born the Covenant.

The Covenant then proceed for the next 3300 years to expand their borders, encountering new races, and in almost all cases, making them submit and join the Covenant on their Great Journey (the search for the Halo artifacts in the hopes of triggering them and wiping out all sentient life in the galaxy...again...because this would take them to heaven). And then they came upon us.

Humanity developed Slipspace technology late in the 23rd century and for the next 230 years rapidly spread out from Earth, establishing hundreds of colonies. But by the start of the Human-Covenant War many of Earths colonies were feeling a longing for a bit of self rule, giving way to a pretty sizable insurrectionist movement. And so were the various SPARTAN programs conceived. Designed to be special forces groups that could quickly quell rebellions by taking out their leaderships. First genetically modifying and augmenting adult special forces volunteers for the SPARTAN-I program. Then kidnapping children with excellent genetic profiles and rigorously training them from age 6 to 14 and then genetically and physically augmenting them. And finally, sometime after the start of the Human-Covenant war in 2525 (the same year the SPARTAN-II's graduated), probably a decade or two, the SPARTAN-III program was started, mostly using orphans from the various destroyed outer colonies.

Ok, so why exactly did the Human-Covenant War begin? Mainly because the High Prophet Truth (essentially the leader of the Covenant) thought that Humanity were in fact Forerunners, or at least the descendants of the Forerunners, and that if knowledge of this were to spread among the rest of the Covenant it would tear their ideology apart. After all, we would be like unto gods to them, and would seemingly have to have been given dominion over them, and the Prophets weren't all about that. So, instead of offering us a place in the Covenant as they did with all other species, they embarked on a course of genocide, in the hope of wiping out humanity and any evidence of a connection between us and the Forerunners.

How we really are related to the Forerunners is a matter of some debate. There is evidence scattered throughout the various media for and against us being directly related to them. At the very least though, they saw us as their inheritors as guardians of the galaxy, the role they had formerly occupied. This alone would really be enough to make us have a place of honor in the Covenant, above an beyond that of the Prophets, and so whether we were directly related to the Forerunners or not is a moot point, as we were still a danger to the leadership of the Covenant.

As to how and why the Covenant were able to make it to Reach, the UNSC's most important world besides Earth itself, they were able to attach a small tracking device to one of the ships which survived a previous large-scale battle with the Covenant (one of the few we ever won, since the beginning of the war Humanity was always at a severe disadvantage, tactically we were superior, but in every other way the Covenant had the edge, technology, weapons, numbers, etc..) which, despite the random slipspace jumps required by the Cole Protocol, allowed the Covenant to find Reach.