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 . <EOS>