A transport system within a fabrication system. The fabrication system contains a plurality of tool bays, each of which has a plurality of processing tools for processing articles. The transport system contains a plurality of intrabay transport subsystems, an interbay transport subsystem, a plurality of stockers, and at least one linking subsystem. Each intrabay transport subsystem is dedicated to transporting articles within a particular tool bay. The interbay transport subsystem, linking the tool bays, transports articles between the tool bays. The stockers, located between the intrabay and interbay transport subsystems, store articles between processing and transfer articles between the intrabay and interbay transport subsystems. The linking subsystem, located between two adjacent intrabay transport subsystems, provides direct transport between the two corresponding tool bays.