When Mammoth Mogul stole the power of 11 Chaos Emeralds from the super being Enerjak, he transported Sonic the Hedgehog, Tails and Knuckles the Echidna to an alternate Zone. They managed to escape the zone however, and the powers of Power Rings, Sonic and Knuckles transformed into Super Sonic and Hyper Knuckles, while Tails managed to transform into Turbo Tails with the help of Athair and the Ancient Walkers. With their combined powers along with help from Athair and the Brotherhood of Guardians, Master Mogul's powers were utilized and transformed the power of the numerous Chaos Emeralds into a single Master Emerald, with Mogul trapped within. This new massive Chaos Emerald was then used to maintain Angel Island's low orbit of the planet Mobius.
When A.D.A.M. enacted his plan to draw all of the Chaos Emeralds from around the universe to Mobius, his plans ultimately allowed Tails, the "Chosen One", to fulfil the prophecy of producing the Great Harmony. While A.D.A.M. was distracted, Shadow assisted Tails and opening a portal to the Zone of Silence. There, Tails sent all of the Chaos Emeralds where they would be safe and out of reach from villains, thus fulfilling the prophecy set out by the Ancient Walkers. When A.D.A.M. was using a captured Shadow and Tails to pull all of the Chaos Emeralds to Mobius, he was perplexed as to why the Master Emerald was not amongst them. The combined effort of Locke and Dr. Finitevus ensured the Master Emerald remained secured on Angel Island.
Not longer after the Great Harmony, Dr. Finitevus managed to con Locke into entrusting him with the care of the Master Emerald while he searched for the Brotherhood of Guardians. During Locke's absence, Finitevus enacted the final phases of his ultimate plan to destroy Mobius by reviving Enerjak and placed a Hex on the Master Emerald. When Knuckles the Echidna returned to Angel Island to assist his father Locke in protecting the Echidnas, he was ambushed by the Destructix and brought before Finitevus. The mad scientist informed him of the destruction of Albion and how many echidnas were alive. With this as persuasion, Finitevus convinced Knuckles to pull energy from the Master Emerald and become Enerjak. The moment he did this, Knuckles became a slave to Finitevus' hex, making his ideals bend to those of the albino Echidna.
When Sonic and Julie-Su arrived on the scene, Finitevus informed them that no one could use the power of the Master Emerald except for Knuckles due to the hex he placed on it. Despite this, Sonic some how managed to use its power to turn into Super Sonic. Which this power, Sonic managed to distract Knuckles (who was presently Enerjak) long enough for Locke to surrender his life and thereby break the hex Finitevus placed on the Master Emerald. With the hex broken, Knuckles returned to normal and forced Finitevus to flee. Since then, Knuckles has vowed to protect the Master Emerald, even if he must do it alone.
Having been separated from the mainland of Angel Island by the battle between Super Sonic and Enerjak, the Master Emerald Shrine now floats a short distance away. The Chaotix bridged this gap during a trip to the island to check up on Knuckles, during which Rouge the Bat convinced the Guardian that he could watch over the Master Emerald and continue to take part in the war against Dr. Eggman without choosing one or the other by using a Warp Ring taken from Dr. Finitevus.