The ending did not make sense. Some say it implied General Thade flew in faster than Leo. The director says it was to be explained in the sequel that never happened.
But the message was good. Today humans consider themselves the greatest and scoff on any chances of any other race taking over. Just as the humanoid apes don't even know that their species was created by humans they now rule over. They can't even imagine the technology humanity has risen to in another planet, thousands of years back in time.
Well, as did we humans, as the Matrix puts it well, spread across, conquer and now rule Earth as viruses are, albeit at a different level.
The age of disaster, will one day happen,
Not I, nor you, can imagine its source,
But destruct it will, what creates it,
and with it itself, in such endless cycle
