I decided to go with the Rule of Three and just discard my first two ideas, which were unicorns as secret harbingers of a worse apocalypse, and unicorns as a warning from Mother Nature about ecological imbalance. My third thought was encapsulated in a comment I posted on Theodora's blog:
"The first title to come to mind was ENDLESS RAINBOWS ON A CLOUDLESS, EVER-LASTING DAY. The first line I thought of was 'On the fifth day, Ellis died, most likely from an overload of rainbows. We decided to go to the lake and give him to the narwhals, hoping to placate them and, perhaps, their earth-walking cousins. No other sacrifice had yet helped to stave them off, or bring any measure of blessed darkness back to the world.' I like the idea of the world itself being transformed by this apocalypse."
After a bit of poking around on Google (between pricing outrageously rare poetry chapbooks), I realized that this was ludicrous; there is NO WAY there would ever be narwhals in Cayuga Lake, even in the event of a unicorn apocalypse. Besides, narwhals are actual animals, and only very pale stand-ins for the unicorn, which here is the harbinger of destruction and remaker of the world. And not in a "back-to-nature" way, but in a "we're tired of being pushed around and made into cute notebook covers" kind of way. The entire way the world works must go, decree the unicorns, and the apocalypse arises from there.
The blend of classical traits and tropes with the current softening of unicorn symbolism seemed like an enjoyable path to take. Unicorns are detectors of virtue, instant healers, and savage fighters. They are hard to kill, not just because of their swiftness, but because, as Holly Black points out, their death shakes the universe. I decided that this was literally true, and what makes the unicorn apocalypse even harder to deal with is that a unicorn's death wreaks earth-shaking havoc around it. Sorry humans, killing them literally does more harm than good.
This remaking of the world, on the surface, might sound compelling or even pleasing. As the unicorns emerge in strength from haunted woods, unknown canyons, and the other hidden places of the world, they spread sunshine and rainbows, flowers and blue skies. But quickly people realize that these new conditions are permanent; the skies are cloudless, it never rains, and it never gets dark. The new flowers act like hyperactive weeds and choke all native foliage out of an area, creating endless carpets of cheerful wildflowers that sink their roots into the earth and climb anything they can't choke into oblivion. They thrive in the everlasting sun, but are sadly inedible to all except the unicorns. Monstrous rainbows appear in the skies, hypnotic and maddening in their omnipresence and unfounded joy. The land masses turn into vast unicorn playgrounds where humans (and indeed, most animals except for the chirpiest of birds and most pleasantly buzzing bee sand dragonflies) can no longer thrive.
Initially human governments try to use coercion, and then force, to deal with the unicorns. But once the first few are successfully killed, the effects of their demise obviously far exceed what little benefit is gained from eliminating one. Some humans go to sea, hoping to avoid this bright, shiny horror of a world. Others retreat to extreme climates such as mountaintops and deserts. A few just lay down in the endless fields of flowers and wait to become fertilizer. Others attempt to figure out a way to fight back, until one day, a young woman asks an odd question: what if fighting them is not the answer?
That's as far as I have gotten.
EDIT: Here is Theodora's take on the unicorn apocalypse. I'll happily link to others as they appear.
EDIT THE SECOND: This was quite helpful as a loosening-up exercise! I wrote about 250 more words on a story and polished up a complete story (cut about 200 words from it, slightly altered the characters' main interaction). I'm debating whether the latter is ready to send somewhere.