Koopatraz State Prison is a highly-secure prison controlled by the Koopa Kingdom.
Koopatraz was constructed around 700 AD to house prisoners-of-war from the Mushroom Kingdom, which was trying to invade the Koopa Kingdom but failing miserably. It was filled to capacity for many years, until other prisons were built to compensate for demand. The conflicts died down over the following centuries, so by the 1950s, there was only one prisoner remaining; Grandpa Toad, who had been imprisoned for an attempt on King Morton's life.
By chance, the next king, Bowser, had a new capital built near Koopatraz. In 1989, Koopa forces captured Princess Toadstool and Toad. Bowser, wanting to keep the Mushroom leaders close, had them sent to Koopatraz, but the clones Brooklyn Mario and Mama Luigi led an successful breakout that resulted in the sinking of the island. The prison remained underwater until the Form Wars broke out and the Koopas once again found themselves in need of space to house prisoners. The prison remained in use this time, and Ludwig van Koopa made it so secure that it would eventually hold Weegee for 9,000 years.
Many years later, they arrested and captured Bill Cipher. They then threw him into Koopatraz. He then used his powers to completely destroy Koopatraz