Hero

The Hero is the character that you are.

The Male hero is Red and the Female is Green

Con gives you His Latias when he obtains his Latios and you, Con and Chloe are seen at the end flying

You are flying on Latias

Con is flying on Latios

Chloe is flying on Flygon

In Light Origin Version when you are flying at the end

You are flying on any Flying types you have in your party.

Con is flying on his Rayquaza( Unseen in battle, it is said he found it just before he became the champion in Shadow Origin. ).

Chloe is flying on her Zapdos ( Unseen in battle, it is said it saved her from Moltres at the Great Volcano ).