As I mentioned in the epilogue's author's notes, Clouded Sky was supposed to be part of a series of 'fics set in the same universe and part of the same overarching plot. There were to be three relatively stand-alone stories focusing on characters who happened to witness or be involved in one of the major events leading up to the last 'fic, which would be very long and finally resolve all hanging plot threads. As that final 'fic is probably never going to get written, and Clouded Sky ended up having a significant amount of content that doesn't get followed through on, I've collected some notes here that I hope will bring some closure to the unresolved issues.
First, with regards to Johto, Raikou, and the skarmory: the legendary wars that first led to the creation of Waytar is about to go in for a redux. What actually caused the legendaries to cease fighting the last time was the creation of a new legendary (a fakemon), one that was able to permanently kill other legendaries. The legendaries that had previously fought one another formed an alliance and managed to seal this new legendary away in another fanregion of mine that was to be the setting for the final 'fic. Afterwards, they were left exhausted and, in many cases, badly injured, their armies broken. They were forced into retreat, and since then an at-times-uneasy peace has held between them.
However, at the time that The Ninetales' Curse takes place (about a year before Clouded Sky), the seals placed on the legendary are beginning to weaken, and its influence is extending into the world once more. A further invention of mine is that each legendary has one or two species of pokemon for which it has a particular affinity, and which formed the majority of their troops during the war. For my fakemon legendary, this is skarmory, and as a result of its growing wakefulness, their reproductive rates have gone up dramatically, resulting in their increased aggression and expansion into unfamiliar habitats. The influence of the bound legendary has also awakened a particular hatred of the other legendaries in them, and they've made many attempts, some successful, to murder various legendaries in recent times. Death of any individual body is only an inconvenience to a legendary, as it can exist in several in once and create a new one without much difficulty, but it takes a long time for a new incarnation to reach its full power, so it is a fairly serious inconvenience at that.
For their part, the legendaries are fully aware of what's going on and have been raising their own armies, further throwing the ecological balance into flux. They've begun working together again, seeking a more permanent solution to the problem of the bound legendary, and the final 'fic in the series would have explored how that played out during the outbreak of the next legendary war.
Next, the ghosts. The ability of ghosts to create soulless puppets out of pokemon by manipulating their pokeballs in a certain way was introduced in The Ninetales' Curse. The implications of this ability are not made clear there, however.
There is a radical, but fairly large, group of ghosts that hate the living and want to eradicate them completely. Most ghosts are souls that strongly resisted passing on, back to the dark plane they were born from, but they often discover that unlife is actually pretty crappy. Although they can still interact with the world to some extent, they are no longer truly a part of it; they always have at least one foot firmly in the ghost plane. They have lost the ability to enjoy much of what makes life worth living; they have a limited ability to feel anything, sunlight burns them, and they often find themselves cast into the shadows of the living, simply watching as the world goes by. A ghost's existence is made still grimmer by the fact that in order to increase in power it has to devour other ghosts or leach energy from the living. A ghost therefore has the choice of remaining fairly weak and barely able to manifest in the world, or prey upon others. One way or another, it must always fear annihilation by more powerful spirits.
As a result of these conditions, and the fact that they persist indefinitely unless absorbed by another spirit or banished, many ghosts develop a deep jealousy of the living, which tends to transform into a desire to eliminate them. Also as a result of their potentially long unlife spans, there are some particularly powerful ghosts who still remember the legendary wars and who can recognize the signs that another is approaching. They plan to strike during the chaos of the new conflict, when the living are already perishing in droves, and make an attempt at annihilating them completely—or at least causing as much mayhem as possible.
Because there are few ghosts relative to living humans and pokemon, they use their ability to enslave soulless pokemon to create their own army, after a group of rotom sabotage the pokemon storage network and create soul-split pokemon on a large scale. While this leaves the ghosts with a fair amount of power at their disposal, perhaps their most valuable assets are the polphades, natives of Waytar and the only kind of ghost pokemon that can possess and manipulate inanimate objects. Over the course of the war, they primarily use this ability to reanimate corpses and infiltrate communities of humans and pokemon, gathering information and sowing seeds of panic and discord within the ranks of the living. There are few of them—thankfully—but they have an outsized impact on the course of the conflict.
It is a polphades, Aelis, that manipulates Tobias into destroying the Shield, thereby enabling him and his kind to join their fellow souls in the war against the living. The ghost had taken over the body of Damien Darksand, who wandered too deep into the Dark Forest. Upon the removal of the shield, his faction, which consisted of most of the ghosts in the area, murdered the majority of the Dark Temple's inhabitants and took their bodies as cover, then left the region and went to join their fellow ghosts in Lavender Town, the seat of their power.
So, that's what's going on in the background of Tobias's adventure. I apologize for leaving it hanging as it is, and take it from me—if you're fifteen and think committing to multiple gigantic 'fics is an awesome idea, you're probably going to be really unhappy with yourself in the future! As a final note, because this story was supposed to connect with the others in the series, it actually contains several references to The Ninetales' Curse and to the other, not-to-be-released 'fics in the series, mostly in the Johto arc. Perhaps you'll be able to spot them, now that you know they're there.