The Counter-Time Experiment was a plan to use the power of the Frozen Flame and the technology of Chronopolis to return to an era before the Ocean Palace Incident in an effort to separate Schala from Lavos.

Having been flung into the future by Schala, Belthezar constructed Chronopolis, a time-research lab in the Sea of Eden to work back to freeing Schala. The Frozen Flame was selected as a power source since it was part of Lavos, and Lavos had near-infinite power. He made preliminary preparations and ensured that the organization would continue the experiment in his absence. He then departed for the modern era, leaving the Chronopolis Chief behind as a curator of the facility. 

The Chief continued to prepare for the Counter-Time Experiment; though he feared both the repercussions of the project failing and succeeding, he nonetheless felt it was imperative to push on. In the year 2400 A.D., the experiment took place; specifically, research group 3B released the Flame's block-level to D in order to trace the counter-time effect. As planned by Belthasar, the resulting catastrophe phased Chronopolis far into the past of 12000 BC. Lavos, awoken in the Ocean Palace disaster, used the Frozen Flame in the facility to do this in hopes of mucking with the timeline. Dinopolis was shifted into the Keystone Dimension by the planet to counter Chronopolis's introduction into the past; once the staff of the time fortress became aware of their surroundings, they dispatched a force to deal with the Dragonians.

The battle was soon won; FATE divided the Dragon God into six components and engineered Elements derivate relics that could produce a natural effect when activated. FATE also aspired to construct its own paradise; though its primary objective was to not disturb history until the future came by not making contact with the Zenan mainland, FATE drew up a plan that would allow it to create its own civilization and preclude any outside contact. It terraformed the archipelago of El Nido and selected several staff members to populate the islands. FATE also devised a system of manipulation over the island's future inhabitants; called the Records of Fate, these machines could rewrite personality and memory when accessed, ensuring that FATE would dominate the lives of its people. The population it had selected was then wiped clean of its memory and dispersed throughout the islands; the Dragons too were stationed in six areas around El Nido. Content, FATE allowed the new culture to grow for the next few thousand years. Chronopolis meanwhile continued to be staffed by a skeleton crew of apparent "ghost" workers.

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