"best system of emission reduction . . . that has been adequately demonstrated" as it typically done with technology based solutions to limit emissions, the EPA decided to implement a scheme that required existing power producers to use "generation shifting" - i.e. they would have to shift generation of power away from coal plants / natural gas plants to natural gas / renewable.

From the sylabus of the opinion"
"In devising emissions limits for power plants, EPA “determines” the BSER (best system of emission reduction) that—taking into account cost, health, and other factors—it finds “has been adequately demonstrated,” and then quantifies “the degree of emission limitation achievable” if that best system were applied to the covered source. §7411(a)(1). The issue here is whether restructuring the Nation’s overall mix of electricity generation, to transition from 38% to 27% coal by 2030, can be the BSER within the meaning of Section 111."

The emission caps the EPA created were not those based on any technology that could be implemented at coal plants, they were based on what the emissions levels would be if the country transitioned from 38% to 27% coal by 2030. This was a novel approach taken by the EPA. The court found that the Clean Air Act didn't authorize the EPA to regulate in this fashion. They can still implement emissions limits, including on CO2, but they can't base the achievable emission limits for coal plants on the overall emission as a nation if coal plants produced significantly less of the power we use.