The Simpsons Movie
When Lake Springfield becomes so toxic that a squirrel, chased into the lake by a raccoon, mutates into having 38 eyes, the EPA steps in to protect the environment by quarantining the city and residents of Springfield under a dome.
Eventually, the EPA convinces President Schwarzenegger to hand over the power to do as they please, where the EPA decides to nuke the city with everyone inside.
> squirrel mutates
https://www.youtube.com/watch?v=d9VriVFtNjs
> quarantine dome installed
https://www.youtube.com/watch?v=RkfOiajHpY8
>E-PA! - Grandpa Simpson
https://www.youtube.com/watch?v=Plr7_SAuB6g