The more complex the better.

Also, I'd like the disease not to be apparent in source, the actions should be whats happening and the players should try and figure out what's causing it.

The first thought the players should have is probably psionic or magic in source, but the scope should be on an epic level naturally.

I think the disease should influence the host, but not directly control them, perhaps give the disease an ego score that grows depending on stage of the disease?

The campaign is going to feature the dreamscape heavily, and the character who is ground zero of this disease can damage people's souls, so that's something to work with...

Phage should go through several stages, which should increase it's ego score, it's mental stats, and a template it applies to the infected.
The template then evolves to become more prominent and has less requirements, such as crossing over to plants, animals, and insects, or creating effects that spread the disease or that spawn manifestations of it such as the disease mutating into a spore-like parasite.