CD releaseThe packaged version on CD-ROM, released in January 2006, contains the game on CD in a DVD slipcase, the soundtrack and digital collector cards. If you had already bought the digital download version, you could order the game for only $4.99. This offer expired on 28th February 2006.
Director's cutIn December 2006, a director's cut version was released, free for all owners of the game, and replacing the existing version, developed in collaboration with the original creator Jeff Smith. Most of the improvements were made to the first episode.
Smith thought the ending of Out from Boneville was a little jumpy and confusing; so he tracked the scenes and wrote new material to explain where everybody was going and why.
The second type of change was to start setting up the larger Bone story to take place over the course of all the games. To do that, an atmospheric beginning called "The Prophecy" was added. It tells the story of Mim, Queen of the Dragons, and her battle with the Lord of the Locust, setting the stage for the Bone cousins' arrival. Things seen in the Prophecy are meant to reverberate throughout the series. There were no changes to the actual games or puzzles.
There are also technical tweaks, such as scalable resolutions and better game stability, and added dialogue lines to improve story flow and enhance character development. It also features updated voice acting and character model for female protagonist Thorn, to more closely resemble her characterization in The Great Cow Race.
Heather Logas made a movie version of the game for Smith. He was able to watch the game as a film and figure out where the weak spots in the story are. Based on this, parts were rewritten for the director's cut.