The difficulty of hunting had increased, but the clones still thrived thanks to this situation. There could have been peace, but the pantheons were greedy for divinity. It just so turned out that a pantheon was a large coalition of sources of divinity. It was too large for them to ignore.
Large pantheons hunted small ones, and two or more pantheons ganged up on another. Legion followed along like vultures following the trial of destruction created by war.
Their specialization in various stats and their perfect corperation helped them to survive between the large teeth of Pantheons. The addition of a weapon that can change shapes and be used for both attacking and defending, and the spear that uses Authority made them stand out and thrive.