^ Before writing anything on Mega Evolutions, maybe you should wait until X/Y come out for more info?
This. Difficult to work with canon if there's very little information out about it. We don't even know the exact canon explanation for how Mega Evolutions work.
Also, about the "Pokémon mixed with the Aquino assassination" plot, er ... please don't. I know that sounds harsh, but dude, wasn't the assassination a terrifying time for everyone involved? Filipino civilians had no idea what was going to happen, and they were fresh on the heels of a period of martial law that was instated to silence political opposition. There's a reason why there was a massive uprising afterwards. And even then, integrating a non-serious franchise with such a serious moment in history almost feels like it's making light of pretty powerful events. I know you're Filipino and therefore proud of your history, but as someone of Filipino heritage myself and whose family was
there during Marcos's reign, I'm a little antsy about seeing such a nerve-wracking moment of history be portrayed in a fanfiction for a franchise centered around magical monsters. I mean, seriously. Civilians
died during that time. A
lot of civilians.
Besides that, not everyone knows about Filipino history, and I don't think plopping Pokémon smack in the middle of one of its major events would be a good way to teach folks here.
That said, on to Keizaal's idea.
Right off the bat, I notice something you may need to take into consideration.
making every Pokemon in Unova weaker, giving them the ability to die.
... The fact that
can already die, and they have for quite some time. That's true in every known canon, actually. In the games, it's a major plot point in Gen I and FrLg (with Pokémon Tower and the ghost Marowak), and you're required to visit Pokémon graveyards in at least two other generations. (You need to visit Hoenn's Mt. Pyre to obtain the Red or Blue Orbs, and both BW and BW2 have you visit Celestial Tower to advance to another gym.) Various manga revisit these graveyard locations, and the anime even has the balls to step forward and give us movies that show us
legendary Pokémon are mortal too. (Latios and Darkrai in particular. Celebi nearly dies as well.)
To be frank, the reason why death is never explained (in the games, at least) is entirely a meta reason, although the games seem to imply that battles never use killing force anyway. Note that every Pokémon that's knocked out in the gameverse is considered to be
fainted, not
killed. It's like a boxing match or martial arts fight for them. Yes, you aim to hurt, but you never aim to
kill, even if you
could. (The anime, meanwhile, runs purely on cartoon logic and is inconsistent about this matter, and Special is straight-up, "The **** do you mean Pokémon don't die in battle?")
Tl;dr, right off the bat, you're on shaky territory canonically if you don't mind me saying. While you could always go the historical route, you'd have to make this an event that happened eons ago, before the events of pretty much any canon. And even then, the idea of having a constructed virus might be a bit too scientifically advanced for a far-flung past, and I'm not sure if explaining it with "this came from a lost society" would help. That and you'd have to give up using Colress and the protagonist of White 2 because it's also canon in
that universe that Pokémon die. (See Celestial Tower.)
I also agree with Silent_Vibrava about talking Pokémon. Every Nuzlocke does this, but it's very rarely necessary. At best, it makes the Pokémon seem like humans in animal suits, and while it helps a reader connect with these Pokémon and feel even more overwhelmed by their deaths, this is also the easy way out. I'd hate to be blunt about it, but yeah. It takes a lot more effort to make a reader feel something over a non-sapient character's death, sure, but a lot of Nuzlockes seem to forget that there's a
reason why death affects us so much. The focus of the death should really be on the
why part of the way death affects us, not on the fact that we're losing something that can talk. That and, honestly, if you succeed in getting someone to cry over an animal's death despite the fact that it's an animal, what that says is you've got an extremely powerful bit of writing that relies on tone and character reactions. In other words, when you kill off a non-sapient character, you're forced to highlight the reactions of the survivors, so our attention hones in on the way this death would affect the trainer.
Moreover, at the same time, the explanations for these kinds of things just feel either forced, Sueish, or nonexistent. In this case, the explanation could be a bit shaky, depending on how old the device is. If it's a widely distributed piece of technology, sure, it might be fine after a bit of tweaking, but if it's a new invention, one has to wonder why Silph is exporting all the way to Unova. That and not every Pokémon
has a neck, meaning this already gets awkward for Pokémon like Magnemite. Finally, there's the question of how it works, given the fact that you'd have to program
every last word in whatever language you're using into the device, plus you'd have to figure out a way to drown out a Pokémon's natural cry. You might be able to get away with handwaving all of this in any other genre, but considering the fact that you're going for a sci-fi edge, you
would need to put together an explanation.
In short, it's an interesting idea on the surface, but there are a few fundamental issues/canon contradictions to it that might not allow it to work. If you want to go about writing a story in which a virus decimates the Pokémon population, that'd be an interesting thought, but if you do it, it would be better to avoid bringing in the idea that this pandemic suddenly gave Pokémon the ability to die ... because they've always been able to do that.
And seriously, while it's ultimately up to you (because you can also make a talking Pokémon's death dramatic), I'm a bit skeptical about whether or not it'd be necessary here.