After Dimitri was buried beneath the ruins of the original Nekronopolis, the High Council of Echidnaopolis made his brother Edmund the first Guardian, entrusting him with the protection of their city and the people. Their first act was to declare a ban on all excess technology, with the hopes that it would prevent another machine such as the Chaos Syphon, which had driven Dimitri mad, from being created. Many citizens complied, but those who refused to give up the technology of their heritage joined together under Dimitri's son, Menniker, to become the first generation of the Dark Legion. The technology that was collected was stored in the Grand Conservatory, which was then sealed up.
The Grand Conservatory would later be breached by the Dingoes, who stole nuclear weapons the Echidnas had built centuries before with the intent of turning them against Echidnaopolis. Guardian Hawking, taking plans from the Conservatory, constructed the Hyper-wave Projector to transport Echidnaopolis and the other inhabitants of Angel Island to separate zones after thwarting the assault, needing time to clean up the island from the nuclear fallout.
Knuckles the Echidna would later penetrate the facility created by his ancestors after Archimedes brought the Chaotix to the Grand Conservatory in order to lure Knuckles there. After breaking through a series of highly advanced defenses, Knuckles found his friends safe-until Enerjak, emerging from beneath Mt. Fate, took them prisoner and banished Knuckles and Archimedes to Sandopolis, moving himself and the Chaotix to the new Nekronopolis at the same time. Later, the Dark Legion would seize the Grand Conservatory as a base while preparing to unleash the Quantum Beam weapon on Angel Island. Their occupation was broken up by a Brotherhood attack led by Guardian Mathias, who ended up dying during the assault as the Quantum Beam was fired.
Later, the Brotherhood would use the Conservatory as a hiding place for a weapon designed to kill Enerjak if he ever was reborn, which Locke sought to recover when Knuckles was brainwashed by Dr. Finitevus into taking on the role. Aided by Sonic the Hedgehog and Julie-Su, he broke through the Destructix, Scourge the Hedgehog, and Fiona Fox, whom Finitevus had set on guard duty. Locke's plans were then ruined when Sonic himself destroyed the weapon, refusing to kill Knuckles just to achieve victory.