The League is the alliance between all Seekers and Monte Cristons, as well as some others, to make sure the Prophecies do not become true. They have made rules that must be followed, and if they are not, a death sentence is given. The League considers Soul Stealers and Pheonix Souls outcasts and betrayals of God which must be taken care of or exterminated.
The League is an order to make sure the Seekers and Monte Cristons stay on track and do their jobs, lest the world come into despair from one of the outcast Souls.
Ultimately, The League considers itself the protectors of Gaia.