I would change the o2 killing weapon to some bacteria thats killing the alge in the ocean since he ocean is where most of our breathable o2 comes from the amazon is the largest landbased source. As well to destroy atomic bonds your talking a fission process o2 isnt a particle but a element.
In order to organise and develop the technologies you suggest a MAJOR power is needed to fund the project. EXP if its not known to the populace.
Ive written quite a few of these eco stories over the years. and watch WAY too much Nova and the like
Oh id as well take a look at using gimp or photoshop to flood the earth with a earth map and a elevation image overlayed. This will give you ideas of places that will be viable to place the story. (would hurt to place it in NY when its under 100ft of water)
Attachment 21311
here is a sample of one I did for some trek pics as you can see most of the east coast is gone. As well as huge chunks of norther europe, not to mention a lack of southeast asia. This map was made with elevation maps only, I didnt touch up anything by hand. It is as accurate as the source maps which I think were 20K wide.
I recomend googling global warming and other science based theory based on pollution.
edit oh I didnt see that poll there. . . I say military if those are the options. Since organisation is the only way to do this with the tech level set to 2020 which would mean the team will have to develop some sort of FTL drive. Because 2020 as we sit now will only have ion drives IF that. Relising this might come across as being on your case. . >_> Im just trying to give tips from experience in writting very similar stories.