 A judge in Mexico has ordered work to stop on a stretch of the Maya train project. Flagship The judge's decision was based on a lack of environmental permits for the project. The train aims to connect archaeological sites, jungles, and beaches of the Mexican Caribbean. It is a flagship project of President Obrador's government. In this example, flagship describes the best or most important thing owned or produced by an organization. As a Navy term, the flagship is used by commanders leading military operations.