Prison Island in this game is what remains of the island that was partially destroyed in Sonic Adventure 2.
Dr. Eggman's bomb caused toxic waste to flood the rivers in the area, and plant life has grown on many of the structures.
Shadow the Hedgehog uses Chaos Control to teleport to the remains of Prison Island in search of another Chaos Emerald. He is then treated to some flashbacks of his cell on the island, raising yet more questions about his past. He very quickly runs into Doom's Eye, who gives Shadow the usual goal of destroying the human military presence in the area. Meanwhile, Charmy Bee (on behalf of Vector) asks Shadow to help him look for five top secret disks. The neutral path sends Shadow straight to the Goal Ring near the end of the stage.
The following weapons can be found in Prison Island:
During the first Air Saucer segment, the player must take the ramp on the left to reach the upper path. The key can be found in a locked container just ahead, which is opened by defeating all nearby enemies.
Following the third checkpoint, in the area with two Gun Beetles and several Black Arms, a key can be found on a platform to the left within a Wooden Container.
Past the fourth checkpoint, the player will go down another river of waste. There will be a large platform to the right of the river; the key is underneath a large panel there.
The final key can be found after the Sixth Checkpoint. The player must the Air Saucer all the way down the river until they come across two Grind Rails. The key is located on the one that begins on the right.
Two Tank Cannons can be found inside the door, which is located past the third checkpoint.
This is one of the few stages where co-op play is impossible- both Charmy and Doom's Eye are unplayable as they fly and don't attack.
This stage is also one of the stages that also appeared in Sonic Adventure 2, as Shadow mentions that he was captured here.
Much like the moon being blown in half in Sonic Adventure 2, Prison Island was also blown up by Eggman and Shadow in Sonic Adventure 2. In Shadow the Hedgehog the island is still there, albeit in heavy disrepair.
If the player has Shadow stand still for a couple of minutes, he will ask aloud whether the two hedgehogs are somehow related.
Additionally, Prison Island's music shares the same main theme as Black Comet, with many similarities.
At the checkpoint after Top secret disk #4, Doom's Eye tells the player to use it to go back, regardless of the current mission character.