Originally Posted by Grassy_Aggron
Here's an idea.
Maybe it's not a team, this time.
Maybe it's the Legendary Pokemon themselves. X could seek to protect life (both males and females have at least one X chromosome) while Y tries to destroy at least half of it (only guys have a Y chromosome).
It could also go with the idea of genetic abnormalities. Perhaps they come to view humans as that...?
That could work, and the side that wants to destroy could be based on the version you have, being if you have X version then X is the side that wants to save life, and if you have Y version, then that side is the life preserver.