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Just took the time to read over this whole idea and then take a look over the comic art itself.

I'll be completely honest here: I don't like it.

First of all, the plot idea. The explanation of why there are animal anthropomorphs is more than just a bit far-fetched. If Gerald's research was shut down by Government intervention specifically because they fear what might happen if the virus is released, why did they not seize the virus and put it somewhere safe?
Furthermore, how the heck does it spread in just a few hours around the entire world? That isn't even physically possible by any stretch of the imagination - you might have noticed the fact that the H1N1 virus (aka swine flu) was only recently declared a pandemic - and it's taken weeks for it to reach that far, and I doubt it's managed to reach every part of the world yet.
Extrapolating on that point - how on Earth does this virus manage to not only cover the globe in a scant few hours, but also only disappear after a few years? The reason I make this point is that you make it quite clear this is supposed to be 500 years in the future - surely medical technology should be fantastically more advanced by then, and easily able to swiftly develop intervention means for this virus?
Also, going by the fact this virus covers the globe and infects most of the population, I'm assuming this then means a huge percentage of said global population dies soon after. And then there's a civil war? (Also, you may wish to check your history books. I'm pretty sure the name "The Great War" has already been taken for an earlier globe-spanning war or two...)
Then we move on to the year 3000... why?
This next part I have huge problems with. Are we to take it Julian keeps his brain backup on his person? Also, why is he working on maintaining the Swatbot by himself if there's the possibility of it killing him? And the really problematic part: why on Earth does the backup require Julian personally to inject something into a computer? Couldn't someone else have done it when they came in the next morning and found him dead? It is just a computer copy of his brain algorithms after all, right? And the worst part, how the bloody hell do you manage to inject something like this into a droid instead of a computer?! Even for a dying man with a weakening state of mind, it should not be that difficult to distinguish a supercomputer (which is usually huge and occupies a space of several square feet) from a robot (the ones you're describing here sound to be roughly the size of a human).
And then we have the fact that Robotnik, once incarnated, randomly decides to attack New York for no reason whatsoever.
Finally we have Sonic himself, and he's so horribly clichéd I don't even know where to begin, but he reeks of Mary-Sue.

That's before I got to the comic art itself, and there is one thing I will state very clearly from the start: you need to leave the damn Photoshop filters alone. The only thing you've actually drawn on the cover page is Sonic himself, and it's blaringly obvious from the get-go. Regarding Sonic himself, I see what you're trying to do by adding lines to portray all his spikes, but it doesn't really work - he just looks like he hasn't shaved in several days.
Then we get to the first page, and I haven't even the slightest idea what in the blazes is going on here. There seems to be some sort of bizarre non-sequitir happening in the middle, as the dialogue between the characters doesn't add up with what appears to be happening on the page. Also, the fact that you've added shadows to the characters on what I assume are the walls behind them unfortunately makes them look like cardboard cut-outs, as you forgot to shade absolutely anything else on the whole page.
The one saving grace I have seen is that your take on Robotnik for this does actually look pretty neat - however you'd need to do a lot of work on how he comes into existence for it to actually work.

Overall, the best advice I could give you in regards to what you've done so far would be to take a long hard look over it and iron out all the plotholes in it before even making another page - as some more successful writers and artists have put it, if you can't figure out why or how something makes sense, how is your audience supposed to?
Hope you found the pointers I raised useful - I do like the concept of what you're trying to do, but so far the actual idea for it shows need of a lot of work. If you're willing to put that work into it though then I wish you all the best with it!

It's good to see you're determined with this, so I will perhaps keep an eye on it as you develop it - and keep a watchful eye for how the plotholes get plugged ;p

One other thing - could you do something about using bold font in all your posts? it actually makes them more difficult to read, and it's a tad unnecessary.