The top secret disks each consists of a typical compact disk surrounded by a grey frame. If their name is any indication, they contain classified information.
Five top secret disks can be found within Prison Island. In the Hero mission for this Stage, the player's objective is to find and collect all five disks upon request from Charmy Bee, who was sent by Vector to get them. The disks are found in the following places:
The first one is right in front of the player, just after Shadow meets Charmy for the ﬁrst time.
Take the second fork in the river while riding the Air Saucer to reach the third top-secret disk. If the player does not make it to this path, warp back to the fourth checkpoint.
After the fifth checkpoint, the player will see the Goal Ring and a Dash Ring. Jump through the Dash Ring and Triangle Jump on the top portion to avoid the goal. At the end is the fourth disk.
After getting on the Air Saucer after the seventh checkpoint, ride it to the end of the path where the player will ﬁnd the final disk.
The exact content of the disks are never implied directly in the game, although it would seem that they have something to do with Dr. Eggman, as the Stage that comes after Prison Island if the player chooses to help Charmy is the Mad Matrix, where the Chaotix are investigating and hacking Eggman's computer data.
In addition, it could be meant to recover some of the data from the Space Colony ARK as well. As when they were hacking into the computer, Vector said, "Espio, we need you to focus 'cuz if we don't hurry all the data we recovered will be lost.".