Hey slic, nice job! At 276 words, you've come very close to doing something compelling within the 250 word limit. I like your premise and the world you've alluded to; I like the flashes of character development you snuck in, which I wouldn't call cheating at all.
However, the mechanical execution isn't quite there yet IMHO. I'd like to dig in and just critique the mechanics. IMHO mechanical problems are the easiest to fix--you've already got the difficult stuff down. Nevertheless, I think nailing the mechanics is an important part of writing.
She stands on the deck of the strange vessel and searches for the docks. Gliding over the fiery surface through the rough-looking swells, they approach the shoreline.
This sentence reads awkwardly to me. I'd stick "they approach the shoreline" at the beginning instead of the end. Also, who is "they"? We only know about a "her".
The spires of the glass towers are visible now. The sands out of which they grew silently awaiting the approaching storm.
Again, this last sentence trips my awkward alarm. I
think it's a fragment, but it's been so long since I took an English class of any sort that I'm not quite sure about that. "They would soon be consumed by the approaching storm" might fit the bill.
She urges the ship faster, ever faster, and the bizarre craft responds as best it can. Vertical sails flap rapidly while the scoop shaped oars push through the flaming sea.
Minor nitpick: as you've omitted the preposition before "vertical" I'd also cut the one before "scoop", if only for the sake of consistency.
Technology could never have made the ship she rode on. Its internal workings would mystify the most learned engineer. Clearly, this bizarre craft has been conjured up through magic.
You've already used "bizarre" to describe the ship; having it here feels redundant. I also feel like these three sentences could be condensed to two, cutting a few words in the process, but it's just a gut feeling; I'm not sure quite how.
As a master at turning imaginings into realities, empresses and seers earnestly request her services, nevertheless she propels herself to this backwater village.
At the very least, I'd turn the second comma into a semicolon. Then again, I tend to abuse semicolons, which should be obvious from my piece above.
Nearly there, nearly home, only to have to turn around again and flee the killing storm.
I'd cut either the "around" or the "again". Stylistic preference and all that.
Already it has consumed the Cities of the Plains; the only hope for safety out in the uncharted reaches of Cauldron Bay.
Unless there's some reason for it to be a proper noun, I wouldn't capitalize Cities of the Plains. Also, it sounds like there should be an "is" between the "safety" and the "out".
There is no time to go looking for him, he has to be there waiting for her.
She takes her eyes off of the shoreline and looks again at the blinding whiteness on the horizon, the line of grim oblivion streaked with black sores that flies across the land and annihilates order. A vast destroyer rebuilding the world in its own image of chaos.
I think the first sentence here works better as the start of the next paragraph. I'd revise the second sentence like so:
"She takes her eyes off of the shoreline and looks again at the blinding whiteness on the horizon. The line of grim oblivion, streaked with black sores, flies across the land annihilating everything in its path."
The last sentence I would cut entirely. It doesn't carry its weight enough for a word limit this tight.
She sees him! Stooped from age, but waving vigorously, she sees him standing on the jetty.
The second "she sees him" is redundant, but to cut it you'd have to restructure the whole sentence. "He stands on the jetty, stooped with age but waving vigorously."; something like that.
With a sudden wave and a spoken word, he is lifted delicately into the air and brought to the ship even as it turns back out to sea.
The passive voice softens the impact of this, the final sentence.

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Finally, I'm not sure if present tense was the right choice for this. It may be that I've just read too much advice to aspiring writers, but I don't think present tense is a good choice for most fiction. You need a really good reason to use it, and I'm not sure this piece gives you one.
Whew. This turned out longer than I thought it would be when I started. I hope I haven't offended with my nit picking; if you're feeling put upon, feel free to tear apart my piece.
