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Prior to 2269, both segments of Ardanan were largely segregated, with the Troglytes primarily restricted to the plant surface, where they performed the manual labor of mining for zenite. A small but significant group of Troglyte rebels, called Disruptors, arose from this situation, performing minor acts of sabotage and destruction in Stratos.
In 2269, the USS Enterprise visited Ardana, at which time Captain James T. Kirk witnessed the inequalities between these two segments first-hand. It was also during this mission that Dr. Leonard McCoy discovered the detrimental effects the gases produced in Ardana's zenite mines was having on the Troglytes' mental abilities, lowering intelligence and increasing violent tendencies. Over the protests of Ardana's leader, High Advisor Plasus, Kirk approached one of the Disruptors' leaders, Vanna, and offered air filtering technology which would protect the miners from this gas. (TOS episode: "The Cloud Minders")
Now supplied with protective breathing masks, the Troglytes formed their own government, and requested the Starfleet Corps of Engineers's help in terraforming the planet's surface. The City Dwellers, who had broken off relations with the Federation in protest of Kirk's actions, responded by declaring war on the Troglytes. They killed the Troglyte High Advisor, and launched numerous assaults on the surface dwellers, using their transmat technology to launch sneak attacks and then quickly escape any counterattacks.
The new Troglyte society was nearly destroyed, before they gained new leader, a descendant of Soske Busk, the builder of Stratos. He was able to seize control of the Stratos Dwellers' transmat network, leading to a mass invasion of the city. The government fell, and Stratos itself was abandoned.