While agencies have an important role in the interplay between central government and states, their functioning impacts both separation of powers and cooperative federalism. Unorthodoxy in rule-making process serves as an example for the ways agencies can further exploit their privileged position in the frame of government. A reaction to an expansion of the weight and centrality of agencies’ decisions consisted in introducing pieces of legislation substantially downsizing agencies’ rulemaking, and in reconsidering judicial deference towards agencies’ determinations. The paper central claim is that all the three branches of government are showing to some extent a willingness to crack down on agencies: the judiciary through employing preliminary injunctions and reshaping the deference doctrine, the President and the Congress through reforms reducing the space of agencies’ actions.