A storage system and methods for operating a storage system are disclosed. The storage system includes a storage system assembly positioned at a height that is greater than a height of a tool used for loading and unloading substrates to be processed. The storage system locally stores one or more containers of substrates. The storage system assembly includes a plurality of storage shelves, and each of the plurality of storage shelves have shelf plates with shelf features for supporting a container. Each of the plurality of storage shelves are coupled to a chain to enable horizontal movement and each is further coupled to a rail to enable guiding to one or more positions. A motor is coupled to a drive sprocket for moving the chain, such that each of the plurality of storage shelves move together along the rail to the one or more positions. The rail has at least some sections that are linear and some sections that are nonlinear and the sections are arranged in a loop. Example configurations of the storage system can include one or more of stationary shelves, extended horizontal tracks for hoists, conveyors at the level of the storage system assembly, and a manual loading station. The hoist, with an extended horizontal track can therefore interface with the manual loading station.