A storage and retrieval system is provided that automates the process of handling a mixed inventory of palletized and containerized items. The invention is particularly useful in handling cargo and weapons within a ship's hold or magazine. When used on a ship, the invention provides for the stowing and unstowing of loads quickly and efficiently, to automatically secure such payloads for sea and to achieve high stowage density, while retaining the capability to select and retrieve any ordered payload, move it to and load it on elevator trays under computer control.