A lot of my stuff really falls into this category, so I'm going to share the original plan for my 2009 NaNoWriMo novel, as it really turned out quite different.
I originally got the idea about a year ago, as two Gaia-related events set it in motion. First, the evolving item Nartian Rock had its third (I think) evolution, and I fell in love with the character, Kink, for the first time, and instantly equipped his strutting pose to my avatar. Second, it was Easter, and Gaia's event that year involved finding 500 eggs. Since the eggs only showed up about once a minute, I was on the site quite a bit, and eventually, seeing my avatar so much and hunting for eggs gave me the idea for a story.
The protagonist, Bunny Watson (named after a character from Desk Set, which I had just watched at the time) is chosen by an alien, Em, to be his partner while he collects "eggs" (I never quite settled on what they were) that have to be stored inside her. The "eggs" were usually found at events in her community, so she'd have to try and get Em there and keep him secret while still giving him the freedom to find the "egg." In the course of things, she ended up getting a boyfriend, who thought that she was the alien, but didn't want her to know he knew.
I never really fleshed out why the "eggs" were so important, but they had some kind of powers, as Bunny could tap into them to reach a sort of dimension where, if she wanted, she could make herself 50-feet tall. At one point, Em tried to tap into the power of the eggs and ended up comatose, which brought on the appearance of a few other aliens, Elle, En, and Cue, in order to snap him out of it.
In the end, the story I wrote for NaNoWriMo last year had only the most basic elements from the story I originally came up with (a girl has to harbor an alien), and a lot more emphasis was put on Bunny's roommate, who in the original story actually interacted with Em quite a bit more (in the sense that she basically hated him and he had to work hard to get in her good graces), but wasn't in the story as much.