A young boy named Ash ketchum was playing in the woods near Pallet town dreaming of the day he could become a trainer. He then stopped when he felt his tummy growling.

Looking around he saw a bush near a river with berries. With a smile he picked the biggest one he saw, and swallowed it whole.

"What is that?" Ash wondered feelings tingle over his body before falling backwards as he disappeared. 

He was lucky. He shrunk out of his clothes and landed on a stick sticking out of the river while his clothes landed around and got washed away in said river.

"Wha...what is this?" Ash asked seeing how small he was. "Focus you got to get help."

Ignoring his nudity Ash started walking up the stick, which due to his incredibly tiny size was easy, however before he could get bland the stick broke free from where it was stuck and started floating down the river.

"No!" Ash yelled as he was carried down the river. Unable to reach land Ash tried to paddle but couldn't even reach the water from the top of the stick as he was carried away, until he eventually passed out in the middle of the night.

The next day he woke up and saw he was in the ocean, big at normal size was now huge, and worse he was sent flying as a magikarp bumped into the stick from underwater.

Looking down Ash saw he was about to land next to said magikarp when he splashed down.

"Karp?" The magikarp said as it was lost and looking around. Meanwhile Ash struggled to the surface only to be hit by the scales as Magikarp looked around before Ash managed to grap onto a scale and worm his way between them, finding to his happiness that the scales had caught some air between them so he could breathe, as the Magikarp dived back underwater and headed the wrong direction, trying to get to Vermillion, but heading to Johto instead.

Several days later with Ash barely surviving on the unaware Magikarp, they had made it to a place called Altomare. And Ash was admiring the view from the top of Magikarp's scales when he saw a figure in the water heading right for them, revealing itself to be a pokemon with red feathers and sharp teethAsh did not know, but was named Latias about to eat the Magikarp. He tried to jump off but it was too late.

The magikarp was a runt, and was small enough that Latias swallowed it whole, sending both it, and Ash into her stomach where the Magikarp began to splash around trying to escape,  only succeeding in knowing Ash off where he slammed into the wall of the stomach before falling, dizzy, into the stomach acid which made short work of him before he could even feel it.

He expected that to be the end, but would wake up sharing control of the body with Latias, who had absorbed his entire soul, and they now shared the body, memories, and everything while having to work out how to control the shared body while keeping it secret from the overprotective Latios brother that would not like a former male sharing his sisters body, especially since it is only former because his sisters body is female. Though since that did not include any more size changing, that story is not for here.