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I'm not sure what I was thinking.
In the beginning, there was only Arceus. The Original One, alseep and dreaming. First he dreamt of Truth, and Reshiram was born. Second, he dreamt of Ideals, and Zekrom was borm. He dreamt of a murky third, but it could not exist without the melding of the two disparate brothers, who could do nothing but fight for supremacy. From Reshiram came Groudon and from Zekrom came Kyogre, who fought one another as their father-mothers did, creating the world from Earth and Water. When they had fought enough and tired, resting after cataclysmic battle, their Third could come about and give air as Rayquaza, though existence could not truly happen yet.
From Reshiram came about Dialga, and the first moment in time was born. Dialga was unbound and free, and with it Time did not have any meaning, for it flowed wherever it wished without reason. Existence however had a small bit of meaning now, and other beings could take some shape, though they still had little reason or clarity. Reshiram saw this Truth, and it was good. Mere concepts could not truly exist in existence, so as Time was bron Reshiram fell deep asleep and faded away. Zekrom, however, wanted more. He had Ideals he wanted to implement, and so in his own final moments, Zekrom begat Palkia and sent him to destroy Truth.
Palkia sought Dialga out had did terrible battle with him. Dialga's heart was torn out and planted deep within the world, where it would forever beat, while Dialga would be trapped and no longer could he move as he liked. As his final act of vengeance, Dialga charged at Palkia, tearing out his lungs and burying it with him. The victory ultimately belonged to Palkia, however, as his breathing would add to the beat of Dialga's heart, solidifying the space and time around them, imprisoning Dialga forever with him. Their Third, Giratina, was once again born like Rayquaza before it, but was kept at bay as his Mother-Fathers were imprisoned, and him with them.