I'd say it was something along the lines of we started colonizing outside of our solar system/galaxy and came across the aliens homeworld unfortunately as we hadn't previously encountered any real threats on other world we were completely unprepared for an attack. Those who survived the assault retreated back onto the ship, and left the planet. Unknowingly they had picked up a few stowaways. They docked at a nearby human world and the aliens began establishing a hive/base on the planet. Eventually most of the humans there wiped out and soldiers were sent in to investigate.
I'd say the beginning was something like that, aliens spread through our own carelessness (I doubt aliens could create an organic ship (Leave SG:A out of this)). Clones were manufactured in response to the threat as we could make limitless quantities of them.
Why did the aliens attack? Perhaps because (Note: imo OM = superbrain that perhaps can listen to radio signals) the OM saw the humans ship as the only way for the aliens to expand, only hope of leaving planet.
EDIT: Asteriods? maybe that's how aliens could spread