I think that if Team Plasma's goal had been to make people fear what they were doing to the environment, and what that was doing to the pokemon, that could have worked. If they had been able to show the people of Unova how waste from Castelia was polluting the ocean/city, how more and more trubbish/garbodor were amassing near major cities, how Nimbasa's light pollution was affecting the natural world, how Driftveil's mining was destroying habitats, releasing dangerous chemicals and contributing to more pollution from the shipping, and how pokemon battles were expensive, requiring specific facilities dedicated to using a ton of electricity and resources to heal pokemon and then fix up gyms etc...
they might have just been able to control the region. Once people saw all this, team plasma could twist this good cause (of protecting the environment) and made people fear what they were doing. By showing these examples - and showing the possible future consequences, Plasma could have struck fear into the hearts of the masses. Soon enough this would have blown over as we humans are apt to forget instead of heeding the warnings given to us... and then Plasma would have staged a disaster. One of region-wide affecting proportions, this disaster which they'd say was based on climate change, would tear the Unova region apart, creating an apocalyptic Unova. But, out of the darkness, a hero would rise. A hero whose ideals/knowledge of the truth could unite Unova. Team Plasma's king and the hero of the entire region would be able to assume control over the region, and team plasma would have control along with him.
As for what kind of disaster do you say? They could use their trubbishes (and sandiles/scraggies with sludge bomb) to spurt poison into the rivers. Their trubbishes/scraggies/purrloins/patrats could create a region-wide drought if enough amassed in areas throughout the region and used sunny day. Similarly, these trubbishes/scraggies/purrloins/patrats could create floods with rain dance, with the patrats creating thunderstorms using thunder. (all could be blamed on us humans)