There's a book I read that I've forgotten the name of. It was sci-fi about archaeologists at a dig site finding alien artifacts. At some point giant ships emerge from holes in the earth and wipe out most of humanity. The aliens had been on earth for centuries molding humanity how they see fit. I'm sure one of them acted like a Roman or was from the Roman era.
The remaining humans are farmed by the aliens, I think for meat, but a few humans hide and live in the forest. When the aliens start to terraform the planet the new plants grown allow a human male and his son to grow super strong to fight alien troops and ambush the human farms and the giant machines terraforming the planet.
Later he meets engineers who build him a device to take down one of the ships (I think). He somehow gets off the earth and goes to another planet to fight for the aliens who invaded earth because there is a worse race fighting them.
The author had two initials then a name e.g. 'E.L. James' or something like that. It was a trilogy of books; I just can't find the name again.