When Kitty goes to Logan's gravesite to tell him, he's gone from there as well.
The Reavers have their eyes set on obtaining his body, so they invade the site, only to be stopped by the X-Men, but when the dust settles, it is revealed that the shell is empty and they leave. The shell stands remaining as a place for all others to come and pay their respects to him. Though firmly encased in adamantium, Kitty Pryde phased Logan's body out of the shell and had him buried in a secret site, known only to the X-Men and Logan's closest friends.
In this first 'Hunt for Wolverine' Volume, we begin the story with what happened since his death.