Dialga, Palkia, and Giratina represent, and overrule, the main components of the univese. Dialga controls time (when), Palkia controls space (where), and Giratins controls matter and antimatter(what). Matter, especially when compared to the stable existence of time and space, is highly chaotic, and so is giratina. Giratina was banished to the distortion world for causing chaos, and now rules as its sole resident. The chaotic distortion world contains antimatter, matter's even more chaotic form that explodes with matter on contact. So, giratina is the ruler and embodiment of chaos, as well as the master of substance.
But that's just my favorite explanation.