SEED is an eco-terrorist organization masquerading as a civil defense organization for the sake of funding and public image.Their goal is to expose the corruptness of modern technology-based civilization by inflicting as much human misery as possible upon an advanced industrialized nation (Japan in this case). They do this by having their psychics like Chris direct the Raaja, which they might well have created themselves, into acts of destruction on critical human infrastructure. After a significant amount of damage is caused, they bring in their unwitting Magical Girl pawn Juna to put a stop to things, thus making SEED look heroic in the process. After all, the public and the media can see SEED choppering in an arrow-shooting warrior to save the day, but they can't see Chris magically/psychically controlling the Raaja from behind the scenes. The development of petroleum-decomposing bacteria (PDB) poses a major threat to SEED's worldview — it represents a risk that the human science and technology they hate so much might significantly repair humanity's damages to the environment. Therefore, they had to take drastic action. By causing Raaja to fuse with accidentally-leaked PDB (which had leaked out because SEED sent Raaja to attack the production facility), SEED managed to send Japan into a state of total blackout and squalor. Once again, Juna saved the day in spectacular fashion, but SEED rests easy knowing that no one will attempt to create or use PDB again.
WMG / Earth Maiden Arjuna