The plug nozzle is one of the advanced expansion devices proposed to improve the overall performance of launcher liquid rocket engines. The present work investigates the three-dimensional flow field generated on this kind of nozzle by partitioning the primary nozzle into modules. A linear plug nozzle has been designed together with modules having two different geometries: a rectangular cross section and round-to-square module. Numerical simulations have been carried out considering the case where all modules of the primary nozzle are active and the case where one module is turned off. The solutions are compared and specific three-dimensional flow structures taking place inside the modules and on the plug are identified. The relationship between these structures and the skin friction distribution within the module and along the plug surface is investigated. Finally, the effect on performance of these three-dimensional flow features is emphasized.