In 2013, President Obama established a 12 year research goal to find cures for brain related illnesses. Expenditures for this project from public and private sources are estimated to reach 4.5 billion dollars by its culmination in 2025. This article will look at the research priorities of the government agencies that are leading the BRAIN Initiative. Based on this information, and actual objectives of funded studies, it is clear that the BRAIN Initiative is ignoring the cutting edge science about multiple brain centers in the human body that comes to us through alternative medicine. Instead, it is focusing on a limited view of the brain that fits in with the agenda of conventional medicine and Big Pharma. In later years of the BRAIN Initiative, there will be a high need for large numbers of human research subjects with impaired brain functioning. These people will be needed for clinical trials of new devices and drugs. This need opens the door to recruitment abuse in a group of people who may not be able to give true informed consent. Even though the tools that will be developed by the Brain Initiative promise to help control a wide range of illnesses with emotional, memory, and cognitive symptoms, the new technology could be used for other purposes. A long list of benefits are being touted by researchers as they discuss their plans to freely activate and deactivate brain cells and multiple sets of cells. One must wonder whether these same tools could eventually be used for other purposes. Could they become tools for aggressive interrogation or mind control?