Off the top of my head I'd say the fly was carrying parasites. So those maggots weren't fly maggots but the maggot-stage of some other insect.

But I'm only guessing - I ain't no stinkin' entomologist!

Good news. It doesn't sound like you made the top 5 -

http://www.cracked.com/article_15816_5-most-horrifying-bugs-in-world.html

Too much spare time on your hands, dude.

Maybe you smooshed open the fly eggs?

It was possibly pregnant:
http://boards.straightdope.com/sdmb/showthread.php?t=473407&highlight=maggots

Possibly parasitized by a member of the Ichneumonidae.

Second the parasite explanation. That's a common situation. They would look thinner than a fly maggot - like little white threads.

You fucken nazi...

I'm going to learn how to pray so I can pray every night that I never, ever, ever have that experience.

Wow. Your building lets you keep dead horses and live maggots? All we're allowed are cats.

Now with Google and Wikipedia, it is no longer acceptable to say "I don't know."

Dude, maybe you're a zombie.

Eggs become larvae inside the body. What you witnessed is the larvae.

One time when I was in college we had in the heat of late summer water fighting and roommates with water balloons and water pistols and I retired late one evening with a loaded weapon and a small bomb or two at my side and woke up in the wee wee hours with someone crumpling newspaper at my side but there was no one there went back to drowse and again, and again no one and then the third time I realized - IT WAS IN MY EAR!
Lightning quick I pulled my sidearm up and aimed right for the nasty creature, drowning it, but no, it scrabbled like fury - FURTHER IN!
Thinking with increased vigor I vaulted toward the bathroom, threw open the medicine cabinet, emptied my gun and filled its reservoir with rubbing alcohol, and again and again pulling the trigger, my little enemy scrabbling increasingly desperately, and then all was silent. Peace. Victory.
My rommate was all "WTF dude?"
Other rommmate was all "Man you shouldn't leave it in there man, you know - what if it rots man?"
Other rommate's girlfriend looked in my ear but couldn't see it. There was wax.
So it was I with a half dozen buttermilk bars and quart of chocolate milk sitting in the hard chair at the E.R. which was relatively small town and quiet and then just as my name came up bang a three-car wreck out on the highway and the attending physicians and nurses were occupied for the next hour and a half or so and the donuts were gone and the milk and when he finally saw me the doctor said
"Have you ever been in a mental institution?" Piercing glance from inches away.
"Uhm...no" Tired donut shyness and confusion.
"Because if I look in your ear and there's nothing there I'm going to have you held overnight as a danger to yourself and the community, do you understand? So if there really isn't a bug in there you can leave now." Authoritative firmness, resolve, restraint.
Hey no sweat thinking donut thoughts of complacent late night youth. Relief.
But what if it fell out or something? Aagghh.
Oh goodness, the tension in that little examining room.
"Oh please please please let there be a bug in my ear. Please let it be in there."
And but yes it was, it was in there still, all pickled in rubbing alcohol.
Nyahh nyahh on you, Doc.
Kept it for a while in a little vial.
It was a weevil.

Jon doesn't keep a dead horse in his apartment. It's a SAVAGE MULE carcass.

Maybe a cross breed, are YOU down wind of Ft. Detrict?

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