Unfortunately, the survivors hijacked it and assaulted Gondor.

Fortunately, Minas Tirith came to the rescue.

Unfortunately, Minas Tirith was a flooded wreck, meaning that it had to crumble, cause the mountains to crumble into the sea and making a wave to stop Mount Zoom, which would take out the rest of Middle-Earth.

Fortunately, the tsunami only hurt the bad guys.

Unfortunately, earthquakes killed all the good guys.

EDIT: 800th post. Yay!

Fortunately, the bad-guys were so traumatised by the experience that they turned good.

Unfortunately, the wave crippled them so they couldn't do a thing.

Fortunately, they were rehabilitated and went out to do good works across Middle-Earth.

Unfortunately all their good works were destroyed by another tsunami and they all figured out being good was a waste of time. So, they turned back to being super-evil.

Fortunaly, they were so evil that they cut each other up.

Unfortunately the strongest among them survived and set himself up as the new Dark Lord of Middle-Earth. Since all the good guys are dead, noone is around to stop him.

Fortunately, having watched Doctor Strangelove [special
director's cut] on dvds, hobbits, nassty elvsees with bright swords,
assorted skinchangers, etc. had prepared underground shelters
so as to avoid a mineshaft gap and emerged to rout the new
Dark Lord and restore Middle-earth (yea! :p ).

Unfortunately, they burned up in the sun because they weren't use to it anymore

Fortunately the valar decided it was time to intervene
again and protected Middle-earth and the good guys
from the sun.

Unfortunately Tulkas decided to nap again giving even the Elves terrible sun burn

Fortunately, Bob the Troll poked him with a spear and woke him up.

Unfortunately, Bob the Troll was crippled and had his head finally torn off by Tulkas before Tulkas went back to sleep.

Fortunately, Bob the Troll cloned himself a million times over before that happened, so there were a million Bob the Troll clones running around

Unfortunately, they were all captured by orcs and thrown into pens where they were chained to walls and poked with sharp sticks.

Fortunately, a terrible monster (named Bubba) ate the orcs.

Unfortunately, he ate them whole and had no stomach acid, so the orcs cut themselves free.

Fortunately Bob the Troll's clones were saved by the alien-eating dog.

Unfortunately, Bubba sure wasn't, and meat was "back on the menu."

Begun the Clone wars has...
 

Fortunately, everyone was content in letting Bubba sacrifice himself for the Bob Clones

Unfortunately, Mount Zoom ran over Bubba and prevented that from happening.

Fortunately, Mount Zoom's front axle broke, causing a huge pile-up with Barrad-dash.

Unfortunately, the two machines both toppled over and crushed all the good guys.

Fortunately, the good guys were so crushworthy that all their fangirls came to the rescue and reconstituted them (with tasty onion broth and just a soupçon of oregano.)

Unfortunately, all the good guys were allergic to oregano.

Fortunately, all teh bad guys died from laughing too much at the good guys dying so everyone died...

Unfortunately, not only was everybody dead, but the good guy's corpses were defiled by fangirl spirit and ff.net evils. This was truly horrible.

"I should have destroyed the world again when I had the chance." Eru was in shock. "I should have destroyed the world again when I had the chance!" Eru pounded his fists in rage on the remains of Middle-Earth, wiping out the rest of the population and causing the still-alive yet endlessly laughing Nazgul and Army of the Dead to be battered by earthquakes and falling rocks.

But Tom Bombadil was fine. Because he's Tom Bombadil.

Fortunately*, Tom Bombadil annoyed Eru enough that he was forced to silence him by dropping him into a bottomless pit of doom.

*Seriously, would you want to spend the rest of your life listening to "Hey dol, merry dol, ring-a-dong-dillo?"

Unfortunately, Thorondor decided to rescue him.

Fortunately, Thorondor was dead.

Unfortunately, Thorondor became a Zombie-King-Bird and still saved them

Fortunately, Tom died because Thorondor smelled too bad, being a zombie and all.

Unfortunately, Tom became a singing skeleton.

Fortunately, the serious cat decided that this thread are too silly for mirth and ate the bird.

Unfortunately, the not-so-serious dog ate the serious cat.

Fortunately, he also decided to use Tom as a singing chew-toy.