Fourteen federal research agencies experienced a sharp net loss of Ph.D. holders in STEM and health roles in 2025, according to a Science analysis of Office of Personnel Management data. Departures outnumbered hires roughly 11 to 1, producing a net shortfall of about 4,224 Ph.D. staff; across agencies the STEM Ph.D. workforce shrank by around 17% on average. Agencies cited retirements, resignations and uncertainty tied to policy and budget changes. The National Institutes of Health saw the largest increase in departures, while the National Science Foundation lost many rotator positions and a substantial share of its pre‑Trump Ph.D. workforce. Observers warn the exodus could weaken federal research capacity, slow grant review and deter academic‑agency collaborations that underpin translational science and graduate training pipelines. Universities that partner with federal labs and rely on rotator appointments should anticipate gaps in research leadership and consider contingency staffing and partnership models to sustain joint projects.