The limited edition bonus CD features three bonus tracks on it. There are two cover songs: a cover of the Pink Floyd song "Set the Controls for the Heart of the Sun" performed by Moore and Portnoy, chosen because they both "love Pink Floyd", according to Portnoy, and a cover of the Neil Young song "New Mama" performed by Moore. The third track, entitled "The Thing That Never Was", is a seventeen-minute instrumental performed by Matheos and Portnoy, showing the original direction they intended to take the album in. The CD contains a 19-minute multimedia section, including two documentary-style videos shot during the album's recording, and a music video for the track "Horseshoes and B-52s" directed by Moore.