Prison Island is a large jungle island used as a prison and research base by G.U.N.. The island had several facilities on the base, including a major port for various military vessels, as well as an armory within the jungle. The main base contained several prisons (hence the name), and also had six levels of security, the highest of which contained Shadow the Hedgehog's cryogenic pod.
Dr. Ivo "Eggman" Robotnik first came to Prison Island to find G.U.N.'s secret weapon, which turned out to be Shadow the Hedgehog. Some time later, Sonic the Hedgehog was captured by G.U.N. due to a misunderstanding and imprisoned deep inside the island, but he was quickly rescued by Miles "Tails" Prower and Amy Rose. At the same time, Shadow, Eggman, and Rouge the Bat attacked the island in order to take G.U.N.'s Chaos Emeralds. They succeeded and planted several explosives on the island, blowing it up as everyone escaped. (VG: SA2/SA2B)
During the Black Arms' Invasion
The explosives had only destroyed G.U.N.'s main base and spilled toxic waste into the rivers. G.U.N. still had some overgrown paths and prison cells in the jungle, and they use them to hold captured Black Arms soldiers. Charmy Bee goes to the island to look for some hidden data disks on behalf of Vector the Crocodile and asks Shadow for his help finding them when they meet up. (VG: ShaH)