Principal agent games are a growing area of research which focuses on the optimal behaviour of a principal and an agent, with the former contracting work from the latter, in return for providing a monetary award. While this field canonically considers a single agent, the situation where multiple agents, or even an infinite amount of agents are contracted by a principal are growing in prominence and pose interesting and realistic problems. Here, agents form a Nash equilibrium among themselves, and a Stackelberg equilibrium between themselves as a collective and the principal. We apply this framework to the problem of implementing emissions markets. We do so while incorporating market clearing as well as agent heterogeneity, and distinguish ourselves from extant literature by incorporating the probabilistic approach to MFGs as opposed to the analytic approach, with the former lending itself more naturally for our problem. For a given market design, we find the Nash equilibrium among agents using techniques from mean field games. We then provide preliminary results for the optimal market design from the perspective of the regulator, who aims to maximize revenue and overall environmental benefit.