When Harry destroyed Tom's diary, that fragment of Voldemort's soul found somewhere else to go... into the girl he was currently linked with.
Launch Flashplayer Download flv (will play with flash players or VLC) (note: This vid is all Aure's fault! She commented that Ginny only loves Harry because she's under some kind of magical influence. I just wanted to play with doing some FX and said I was going to dementor out Ginny's soul. She said I was forbidden to suck the souls out of any of the Weasleys other than Percy. But she never said I couldn't put a soul *into* one of them.
And thus a plot bunny was born. What if back in the Chamber of Secrets, Ginny Weasley became a horcrux? Since Harry is also one, they're literally two parts of one soul being drawn together. It just happens to be Voldemort's soul, because well, I'm twisted. You all should expect such things from me by now. Harry needing to kill Ginny... oh, the angst! Although really, if you think about it, Vegas money is on Ginny winning that fight.)