Journey to the Cerulean Cave:

We were warned to stay away, that Pokemon of terrible power dwelled in the cavern, and didn't appreciate outsiders. But we pressed on. The battles were tough. We were far from the safety of the Pokemon centers, and even our well stocked bags of items were running low. Our Pokemon were exhausted, and though we tried our best, we simply couldn't keep them all in perfect health. Still, we pressed on. Finally, we reached the final chamber of the cave. In the back was the nest of Pokemon eggs we sought. But, there, between us and our prize, we saw the Pokemon we'd read about in Cinnabar. The one which had destroyed the Cinnabar lab with ease. The genetically engineered Mewtwo. And it saw us.


Also, the thing about legendaries not breeding is simply not true. The games have been vague about how breeding works in any case, since no one has ever seen a Pokemon lay an egg. The likely case is that legendaries refuse to breed in captivity, preferring the safety of their own nests. Which are very safe indeed, given how well guarded they are.