Rayquaza is the guardian of the earth's skies, when Deoxys entered the earth's atmosphere (being an alien) he invaded Rayquaza's territory, he then attacked Deoxys. let's say that Rayquaza is the planet's border patrol officer.

This was from the Pokemon movie Destiny Deoxys. At the start of the film Deoxys and Rayquaza are beating the shit out of each other because why the hell not. Mabye Deoxys stole one of Rayquaza's lawn gnomes or somethin', I forget.