A method of operating a transport refrigeration system, wherein the transport refrigeration system comprises: a battery system integrally attached to a drop deck configured to carry a refrigerated transport container of the transport refrigeration system, the drop deck being releasably connected to the refrigerated transport container; a refrigeration unit configured to provide refrigerated air to the refrigerated transport container; and a controller, the method comprising: controlling, using the controller, a plurality of components of the transport refrigeration system, wherein the controlling comprises operating at least one of the refrigeration unit and the battery system; powering, using an external power source, the refrigeration unit when the transport refrigeration system is connected to the external power source; detecting, using the controller, when the external power source is disconnected from the transport refrigeration system; detecting, using the controller, a connection to the battery system when the external power source is disconnected from the transport refrigeration system; activating the battery system when the external power source is disconnected from the transport refrigeration system; and powering, using the battery system, a select group of components of the refrigeration unit when the external power source is disconnected from the transport refrigeration system. a battery system integrally attached to a drop deck configured to carry a refrigerated transport container of the transport refrigeration system, the drop deck being releasably connected to the refrigerated transport container; a refrigeration unit configured to provide refrigerated air to the refrigerated transport container; and a controller, the method comprising: controlling, using the controller, a plurality of components of the transport refrigeration system, wherein the controlling comprises operating at least one of the refrigeration unit and the battery system; powering, using an external power source, the refrigeration unit when the transport refrigeration system is connected to the external power source; detecting, using the controller, when the external power source is disconnected from the transport refrigeration system; detecting, using the controller, a connection to the battery system when the external power source is disconnected from the transport refrigeration system; activating the battery system when the external power source is disconnected from the transport refrigeration system; and powering, using the battery system, a select group of components of the refrigeration unit when the external power source is disconnected from the transport refrigeration system. controlling, using the controller, a plurality of components of the transport refrigeration system, wherein the controlling comprises operating at least one of the refrigeration unit and the battery system; powering, using an external power source, the refrigeration unit when the transport refrigeration system is connected to the external power source; detecting, using the controller, when the external power source is disconnected from the transport refrigeration system; detecting, using the controller, a connection to the battery system when the external power source is disconnected from the transport refrigeration system; activating the battery system when the external power source is disconnected from the transport refrigeration system; and powering, using the battery system, a select group of components of the refrigeration unit when the external power source is disconnected from the transport refrigeration system.