Secrets of the Chaos Emerald is the sixth DVD of Sonic Underground episodes to be released. Published by NCircle Entertainment on July 22, 2008, this DVD consists of four episodes of Sonic Underground, including the entire Chaos Emerald Crisis saga. The total running time of the DVD is approximately 88 minutes.
- Friend or Foe? - Sonic, Sonia, and Manic visit the Floating Island in search of their mother. There, they meet Knuckles the Echidna, the island's guardian, who has been falsely told by Sleet and Dingo that the Sonic Underground are after the Chaos Emerald. While Sonic and Knuckles do battle, Sleet and Dingo set their eyes on the Emerald...
- Flying Fortress - Part 1 of Chaos Emerald Crisis. Doctor Robotnik creates a new flying fortress in hopes of laying waste to Mobius. When the hedgehogs suspect that a Chaos Emerald is keeping the fortress aloft, they head to the Floating Island to enlist the help of Knuckles, who isn't too eager.
- No Hedgehog is an Island - Part 2 of Chaos Emerald Crisis. After taking off with the Chaos Emerald, Dingo steals the Emerald, but accidentally breaks it, unleashing the chaos energy inside. Knuckles seeks out his grandfather Athair for advice on handling the situation. But the Sonic Underground are not prepared for the advice Athair gives them: they must make an alliance with Robotnik!
- New Echidna in Town - Part 3 of Chaos Emerald Crisis. Knuckles bargains with Robotnik in order to recover and repair the Chaos Emerald before Mobius is destroyed, but to acquire the villain's help, the echidna must betray the hedgehogs. After rescuing his friends from the Roboticizer, Knuckles and the Sonic Underground must now combat Dingo, transformed by the chaos energy into a terrifying monster!