The USS John Paul Jones (DDG-53) is a US Navy Arleigh Burke class destroyer that took part in the American counter-offensive in San Francisco in 2027. Over the radio, it can be heard that five Navy destroyers have broken through an enemy blockade in San Diego, and that the John Paul Jones and the USS Milius were en route to assist these vessels in securing the bay.
- The ship is named after John Paul Jones, a U.S. naval hero who fought in the American Revolution. His most famous quote is "I have not yet begun to fight!"
- The radio transmission announcing that the John Paul Jones and Milius were in action in the San Diego area is likely an error on the part of the radio operator. San Diego is 500 miles south of San Francisco, too far for the conventional radios in use by the U.S. military during the battle. The usage of a more sophisticated radio or satellite communications system is also ruled out, due to the GKR's EMP attack that would have knocked out North American satellites as well as ground infrastructure. It is possible that the Military worked out new communication lines before the battles.