DPG suggested that the protagonists be employees of a more mundane government agency. Instead of the CIA, the Livestock & Seed Division of the USDA, hence the bad joke about red meat vendetta. The story of a lowly employee of the Livestock & Seeds division of the USDA uncovering that contaminated meat is reintroduced in the food chain.
However DPG has a good point that there so many government agencies where corruption and deviant behaviour is more likely to take place unnoticed for years. USDA, FDA, CDC, IRS, SEC, EPA, FCC are all agencies with high remit but small funding and limited resources and even less overall supervision.
Maybe those agencies need better advertising. Look at what the TV show NCIS has done for them. In 2000, the US postal sponsored a series of a TV movies about their own investigation services. The movies "The Inspector" and "The Inspector 2" with Louis Gosset Jr were quite decent.
Contaminated food, genetically modified seeds, ineffective medical drugs, lethal vitamin supplements, cancer inducing magnetic radiation, illegal dumping of pollutants, raiding of pension funds can all be great sources of inspiration for thrillers. An innocent person victim of this crime or a lowly government employee stumbling on a nefarious conspiracy. He/she is not necessarily equipped to deal with that. So we have the classic Average Joe/Jane facing the monster and overcoming it.
Well done, I think such movies may resonate more with people than the umpteen super government agent victim of a conspiracy. Steven Seagal, Dolph Lundgred, Steve Austin Direct To Video have all lost their lustre. Compare the success or lack of with the money spinning machine that was Erin Brokovich.