Because I can't say it any better then they do in the Total Annihilation Instruction book and official HomePage:
  Long ago, the galaxy had known peace.
  Paradise was ruled with the hand of science, and the hand was that of the
  galactic governing body known as the Core.

 Ironically, it was the ultimate victory, the victory over death itself, that brought about the downfall of its Paradise and started the war that would decimate a million worlds. The process, which was called "patterning," involved the electronic duplication of brain matrices and allowed the transfer of consciousness into durable machines. Effectively it meant immortality, and the Core decreed the process mandatory for all citizens in order to ensure their safety.

There were many who were unwilling to toss aside their bodies so casually, many indeed who regarded patterning as an atrocity. They fled to the outer edges of the galaxy, where they banded together to form a resistance that became known as the Arm. War began, though it was  never officially declared by either side.

 The Arm developed high-power combat suits for its  armies, while the Core transferred the minds of its soldiers directly into similarly deadly machines. The Core duplicated its finest warriors thousands of times over. The Arm countered using cloning. The war raged on for more  than 4,000 years, consuming the resources of an entire galaxy and leaving it a scorched wasteland.

 Both sides lay in ruins. Their civilizations had long since vanished, their once vast military complexes were smashed. Their armies were reduced to a few scattered remnants that continued to battle on ravaged worlds. Their hatred fueled by Millennia of conflict, they would fight to the death. For each, the only acceptable outcome was the complete and utter annihilation of the other.