New idea,

pan across a city, vultures fly in, every where they fly things behind turn dark and black and become decrepit (use lots of particle effects and saturation levels) close up on flowers and tress dying as the birds fly over there is a special super pretty flower, the vultures gather on power lines surrounding the flower, after a pause they all attack the flower at once, cut to the black as it zooms out you see a bunch of dead ravens and the pristine flower untouched with a ray of light covering it

expanding upon the initial idea

vulture = there head is very similar to the plague doctor mask, they naturally represent death and evil, they can sweep through the city causing chaos yet remaining unseen, just as the plague did.
flower = life, be it human animal or plant its, its a battle between life and death
social decay...... (we all fall down) all the birds fall down maybe the animation is looking at it from the birds point of view(plage/plage dr) but this isn't made clear till the final scene reveal....with the dead birds

"Ring around the Rosie"--refers to a red mark, supposedly the first sign of the plague
- the animation could start with a blood mark on the ground, the camera pans up and shows a bunch of vultures circling above 

"A pocket full of posies"-- refers to sachets of herbs carried to ward off infection, this is the plants in the city, the represent life but also the essence of what was supposed to ward of the plague, but by showing them die represents that this was false hope and wasnt the reality

"Ashes, ashes" --a reference to the cremation of plague victims, line three is rendered as "Atischoo, atischoo"--sneezing, another sign of infection.
-this is where the darkness is spreading, the city is falling apart, a ash like effect could be falling behind the birds 

"we all for down" - the birds are revealed dead and life still lives on 

the great fire is what wiped out the plague, the last flower could be red and yellow and almost flicker with light as the birds are revealed dead the light emanating from the flower will mimic flames