In the late fall of 1945, as Congress began to deliberate about May-Johnson, dozens of young, energetic scientists came to Washington, D.C. to fight for full civilian control of atomic weapons. Most of them had been part of local discussion groups; now they formed themselves into a national organization called the Federation of American Scientists (FAS). The group rented a one-room walk-up near the Capitol, equipped it with a single typewriter, made appointments with Senators and Representatives, sent fact-sheets to committees, and started talking to reporters. One of the leaders, Nobel laureate Harold Urey, called May-Johnson "the first totalitarian bill ever written by Congress. You can call it a Communist bill or a Nazi bill, whichever you think is worse."

They offered an alternative: Working with a Democratic Senator named McMahon they sponsored a bill calling for the creation of a purely civilian Atomic Energy Commission (AEC) to oversee further research, led by a panel appointed by the president, with a civilian administrator and safeguards for independent research. The military was to have no representation. Control was to rest solely with civilians. The debate between the May-Johnson proponents and the McMahon backers continued into 1946, with the FAS firebrands working to make sure McMahon passed. To the amazement of many observers, they won. In July 1946, after the language in McMahon was softened to allow some military input, Congress rejected May-Johnson, passed the McMahon Bill, created the AEC, and handed the scientists a great and surprising victory.