Six U.S. Navy warships will go to sea this year with special software for their Aegis radar system, and SM-3 anti-missile missiles, that will enable them to shoot down ballistic missiles. However, the anti-missile software being used  prohibits the ships from firing missiles at aircraft. Next year, the software that will allow an Aegis equipped ship to take on enemy ballistic missiles and aircraft.

The six ships entering service now will mostly be used around North Korea, the one country that has ballistic missiles and has been most hostile to the United States. North Korea has a lot of warplanes, but few that are trained and equipped to go after ships. In any event, any task force with an Aegis anti-missile ship will have several others that can still take out aircraft with SM-2 anti-aircraft missiles. There are 67 destroyers and cruisers in the U.S. fleet with Aegis systems, and 22 more on the way. 

The navy originally planned to only equip ships with the advanced software, that could handle missiles and aircraft. But president Bush ordered the navy to have their anti-missile ships at sea by 2004, and that meant going with the version of the software that was used to develop the anti-missile capability. Since this was development software, the anti-aircraft capability was ignored, and disabled as modifications were made to make it possible for the Aegis radar to track incoming missile warheads. So, to meet the deadline, the anti-missile only software was deployed while the dual-purpose software is finished.