The powder project was somewhat out of line with Pauling's conventional approach to research and experimentation. He traditionally played a hands-on role in the laboratory, often assuming responsibility for much of the experiment design and data analysis. The nature of the committee, however, interfered drastically with this practice. Much of the research was commissioned out to a variety of groups including the DuPont and Hercules powder companies, various manufacturers of scientific apparatus, and a collection of university and research institute teams. Additionally, much of the data used by the committee was provided by various military organizations or collected through firing tests, a process with which Pauling had little involvement.

Pauling's work was largely comprised of research oversight and organization which was informed by light data analysis. During this time, however, Caltech was involved in an expansive weapons-building project. In the hills around the institute, bunkers were built to house teams of faculty and volunteers that assembled missiles and torpedoes. Parts for the weapons were brought in from manufacturers along the West Coast and then constructed at Caltech. The weapons were then shipped from the bunker facilities to waiting military ships which would then distribute them throughout the Pacific theater. Over the course of the war, approximately one million rockets were built in the Caltech bunkers and deployed against Japanese forces.

As the war progressed, the committee's priorities evolved. Following the initial testing of known powders, the researchers began work on new, hybrid powders that allowed for lower combustion temperatures and greater force. A large program was developed to create and test fire projectiles using a number of propellants with varying properties including RDX (alternatively known as cyclonite), pentaerythritol teranitrate (PETN), cordite-n, and nitroguanidine. Investigations were conducted on projectile designs, alloys for shell casings, and even tapered barrel adapters. Pauling participated in a good deal of experimentation at the Caltech labs, but found himself spending an increasing amount of time in Washington, D.C. attending meetings and conferences. His letters to Ava Helen from this time period, while initially excited and hopeful, quickly became weary and dejected as the constant cross-country train trips took their toll. Pauling was unused to the role of a government administrator and the time away from his family and his laboratory wore on him.