Pauling and his team needed to find a better way to protect invisible inks from being identified when intercepted by enemy forces. To this end, the team began work with substances with high immunological specificity - organic substances that reacted with only a small number of compounds. The team began with a polysaccharide gum distilled from a bacterium responsible for lobar pneumonia in humans. Because the gum was largely chemically non-reactive, the paper it was printed on hid it well. Then they masked the ink with an additional coating of a wax-like substance to prevent all but the most immunologically-specific chemical from developing it. While tedious, the process was effective.

In addition to the use of polysaccharide gum, Pauling and his team examined antibodies and antigens in the hope that they could be used to create inks. In a report to the OSRD, Pauling explained that when a foreign protein (antigen) is introduced to an animal's blood stream, the animal produces a complimentary, highly specific protein (antibody) to neutralize it. When the two proteins combine, they form a stable protein-protein pair. Initial tests of the solution suggested that the antibody-antigen combination could be highly effective. Unfortunately, as they began practical testing, Pauling and his team found it extremely difficult to develop the protein-protein pair without staining or otherwise damaging the paper on which the ink was printed. What's more, some of the antigens could be developed with non-organic chemicals, greatly reducing their security. Ultimately, the antibody-antigen ink was impractical. Pauling recommended that changes be made to the process, but no record of additional experimentation appears in the collection.

Despite success with a variety of inks, Pauling suggested that the project be pushed even further. He explained in a report that, "From the offensive standpoint, it might be considered that the development by the new techniques of substances which are not detectable by the present methods might be useful as a basis for offensive methods." While Pauling made no record of engaging in this process, it is at least plausible that he and his team did in fact note and retain a number of potential developers for future scientists to test.

In all, Pauling and his team developed or enhanced approximately a dozen different ink-developer combinations ranging from the improvements on existing camphor-based Presto pencils to complex processes using albumin, gypsum, and the catalytic reduction of silver. The project appears to have continued through 1945 with the "Final Report on Biological SW" dated December 31, 1945, several months after the Japanese surrender in September.