Cynthia is arceus in disguise and is transexual. If you look closely she never comes to the spear pillar when arceus is there and volo, his brother said he is arceus and you can see this because volo has a tail on his head that looks just like arceus'es.

Volo is male while cynthia is female but they look the same, because actually Cynthia is Volo that travelled in time after you defeat xim at the spear pillar and giratina sends him to the sinnoh of the future.

Then Rayquaza flies into Deoxys' butthole and evolves into Eternatus because they fuse through the infinite energy of the devon SPA.

I played all the pokemon games except LFGG and SWOOOSHI and bdsp and hgss and rgbyr so i know everything about it.