I agree with KoshFan. After the defeat from Valen and Co. the shadows probably dispersed across the galaxy, in all the dark places where no-one would walk. Some probably hid in hyperpace, like the Vorlons had done, since they have a very advanced and seemingly effortless way of moving in and out of hyperspace, and were older than the Vorlons and thus probably capable of achieving such hiding places.
I would assume that some would remain at Za'Ha'Dum since it was their *supposed* home world (Read: Loriens comment about showing respect), and distibuted certain forces in places like Ganymede and Mars, where they would be recovered at a later date.
For the shadows to come back in greater numbers, they would need to manufacture/create additional ships and technology, so there must have been somewhere where such activities took place, and a base of operations needed to collaborate their efforts. Just a Babylon 5 was a center of operations on the side of light, Za'Ha'Dum would be the place of operations for the side of dark. Babylon 5 could not run on it's own without a crew, and likewise at Za'Ha'Dum.
Perhaps hyperspace, the drakh homeworld and the homeworld of the other dark races (it was implied that there were more than one dark servant race, although not mentioned by name). It was also suggested that the shadows in the Valen era were resident on the Narn homeworld, discovered by Ja'Quan and subsequently driven away. The Narns are one of the younger races, so it is entirely possible that the shadows took residency in other worlds without full knowledge of their existence. Who knows, they could have hid themselves at the bottom of the abyssals in our own oceans around 1200 A.D.
Furthermore, the shadows were all about caos, not obedience. The Vorlons would therefore have a clearly defined homeworld and sector in space easily recognisable to others. The shadows would operate a more caotic structure, where their forces were distributed across many worlds, nebula, rifts in space-time, and hyperspace, using natural hiding places or deliberate cloaking. The shadows themselves are not visible to most humanoids, with exception to Telepaths, and could be sleeping in peoples abodes without them realising it.
Telepaths were forcibly introduced into Human genes only 100 years prior to the events of B5, therefore they could feasibly go undetected on earth until this time. Perhaps this is one reason why the Vorlons engineered humans to have telepathic abilities. Maybe the plague was engineered by the shadows to see what would happen. Maybe Jack the Ripper was actually working on behalf of the shadows before being requisitioned by the Vorlons.
Sleep well tonight.
