As most have figured out when they see the English lyrics, this is about Miku being uninstalled from a computer. During that time of being uninstalled, she realized that she isn't a human, but is merely a toy made to imitate one, as it says in the beginning of the song. She needs to say everything she wants to say before she's gone forever, which is why it is a rap. It is rumored to be a song written for a time in 2009 when Hatsune Miku videos were being taken away from YouTube for copyright by a hater group, but that has been proved false, since "The Disappearance of Hatsune Miku" was created in 2007, before all of that happened. The Disappearance of Hatsune Miku has been sung at many concerts, such as Mikunopolis.
There is a counterpart to this song, The Intense Singing of Hatsune Miku.