If you want to kill the final proto-pet, just use the RYNOII. You'll annihilate it before he busts through the floor, or kill'em in less than ten seconds. On planet Oozla, yhe first boss you see, use the Zodiac to obliterate it, or the Ultra Mini-Nuke. On the Marketar Nebula, eliminate the B2 Brawler by allowing him to get down for it's spin attack and blast it with the RYNOII, or the Zodiac.