The penalty is for emissions of pollutants which kill people directly, rather than causing climate change but part of the deal is this:

Under the agreement announced Thursday, Marathon is required to take steps to reduce more than 2.25 million tons of carbon dioxide emissions over the next five years — roughly equivalent to the emissions avoided by taking 487,000 cars off the road for a year, the EPA said in a news release. The settlement will also prevent nearly 110,000 tons of volatile organic compound emissions, according to the agency.