In the ideology of national security, the distinction between war and peace had disappeared in a new era of permanent preparedness that embraced every segment of the nation's society and economy. Needed were plans to harness essential assets to the nation's security and government agencies with enough authority to implement these plans, including plans for the mobilization of science and scientific manpower. Not only that; government had to safeguard economic and scientific secrets by regulating the exchange of information, ensuring the loyalty of federal employees, and guarding against the dangers of internal subversion. In all these areas the national security discourse was essentially a discourse in state making, and the challenge, as in building a new military establishment, was to remake existing institutions or create new ones without wrecking the democratic foundations on which they were erected.

This was a difficult task, in part because national security planners had to take account of established interests, older values, and cherished traditions. Indeed, their quest for authority often challenged the prerogatives of more traditional agencies and groups, not to mention free–market principles and normal government procedures, with results that led to bitter quarrels over how power should be divided, distributed, and held accountable. Economic mobilizers envisioned an operating as well as a planning agency with enough power to override the rights and interests of established authorities. Leading scientists sought a partnership with government on terms that shielded their work from congressional oversight and presidential control.