Michael, the main character, is a high-ranking officer whose part of the Archangels, a small group of highly intelligent and powerful people who govern the clone humans. Unknown to his peers, he's defective and in the process of developing feelings and emotions.
Since the humans of Earth don't recognize or treat the clones as "human", the clones blockade Earth and demand to negotiate human rights under the threat of invasion. Michael is part of the delegation sent to Earth and he, unlike the rest of his peers, mingles with the humans and gets attached to a particular female. When the negotiations go sour and the head of clones attacks Earth, the girl he likes is killed in the first wave of attacks. His newly discovered emotions over rule his better judgement and he alone rebels against the clones and attacks their main mothership head on. He manages to cripple it and it begins a decent down to Earth, all the while fighting the clone commander, Lucifer (who we won't go into detail about yet).
So the ship crashes and was big enough to mess up Earth pretty good. Michael didn't mean for that to happen. He himself crashed on the planet and was taken and held in stasis by a mysterious benefactor. He awoke 500 years later and Earth has been turned into a dangerous, barren wasteland in the most post-apocalyptic sense possible.