The Organization is a group that is shrouded in mystery, even by those who work for it. The Organization controls the Valkyrie- Defiled beings who are capable of retaining their humanity and controlling the demon that possesses their recently deceased bodies. This is possible via a soul bond- the Defiled corpse binds his/her own soul to a living being that shares a bond with the recently deceased person. This person is known as a Paladin.
It apears to be the ultimate goal of The Organization to eliminate the Defiled- though, according to Alan Ryder, it is not out of their compassion for humanity.