Human Extinction Agency (HEA)
The aliens revealed themselves to humanity. They weren't hostile... but that didn't stop them from being the most destructive force ever seen on this planet. They called themselves 'Nacalites', and physically speaking, they were gaseous clouds, perhaps a yard across. They said they'd been silently observing this planet for a bit more than six thousand years, i.e. since before homo sapiens existed -- and yes, the HEA setting does assume that everything human science knows about putting dates to ancient events is wrong. At any rate: The Nacalites had seen humans become an ever-more-destructive blight upon the Earth, and now they could no longer stand by as we continued to wipe out the biosphere which we ought to be supporting and caring for.
The Nacalites' response was simple: Eliminate the human species. Not a destructive species themselves, they couldn't simply kill us outright, but instead chose to transform us all into other creatures. And they set up a bureaucracy, the HEA (Human Extinction Agency), to oversee this genocidal process. For reasons of their own, the Nacalites decided that the transformations should occur in six stages, spaced 10 months apart; a five-year process, at the end of which homo sapiens would be completely extinct. Again for reasons of their own, the Nacalites would allow any transformed person to retain their full human intelligence all throughout the process, if they so desired.
It's not clear from the stories exactly when the Nacalites showed up. However, we do know that work on the film Saving Private Ryan was interrupted by the HEA's activities, which would put the Nacalites' advent somewhere in the late 1990s.
There are various internet archives where HEA stories can be found; this site is one of the better ones.
This story universe was created by Oren the Otter, who reserves the right to declare any concept or story non-canonical for his universe.