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The Isle of Ancients was a major setting in The Subspace Emissary. This is the place where the Subspace Bombs were created due to the advanced technology. The Isle of Ancients is an island suspended in the sky and was inhabited by a group of robots, better known as the R.O.B's. The fact that it's an island that floats in the sky and home to a tribe that's now almost extinct (R.O.B's) could be a nod to Angel Island in the Sonic series.
On the island there is one leader called the Master Robot. It is also known as the Ancient Minister. The other robots gave their unwavering loyalty to the Master Robot and lived in peace. But Tabuu took the entire island hostage. The Master Robot wanted to avoid losing so many of his brethren to Tabuu so he reluctantly agreed to be the main front of the Subspace offensive, and began development work on the Subspace Bombs. The Master Robot then decided to disguise himself as The Ancient Minister out of shame for his own decision to work with the Subspace Army. The Dark Cannons were also being developed and built on the Isle of Ancients. Samus' Power Suit was also kept on the Research Facility here and Pikachu, was captured and kept prisoner as a power supply. Additionally, Ridley was stationed here, but his role was unknown, though given Samus' Power Suit was held on the island, it isn't out of the question for him being placed there in case she came to retrieve it.
When Olimar, Captain Falcon, Pikachu, Samus, Diddy Kong, and Donkey Kong broke into the Subspace Bomb Factory, Ganondorf ordered that all the Subspace bombs be detonated in order to create a portal large enough to fit the Subspace Gunship through. The Ancient Minister and the other heroes tried to stop the inevitable detonation, but ended up fleeing on the Falcon Flyer. Meta Ridley tried to stop them, but they defeated him and escaped. The Isle of the Ancients was engulfed in Subspace.
In the ending (or new beginning) of the game, the spot marked by the shining "X" is where the Isle of Ancients was. When Tabuu and the Great Maze were destroyed, most parts of the world returned to normal, but the effect of so many Subspace Bombs going off at once made it impossible for the Isle of Ancients to return to normal.