While the US Navy is generally immune to IED attacks (the USS Cole tragedy notwithstanding) it must remain vigilant against ballistic missile strikes launched by hostile nations. When that happens, even before the Phalanx system begins to spool up, US warships engage the Aegis BMD—a nearly impenetrable ship-based missile shield.
The Aegis BMD (Ballistic Missile Defense) is a sea-based weapons system for defending against short- and mid-range missile attack while the threat is in its post-boost phase, just prior to reentry. It is designed, built, and operated by the US Missile Defense Agency (US MDA) in conjunction with the US Navy. Aegis BMD is actually an upgraded version of the Aegis Combat System, which debuted in 1969, and is considered an imperative component to the US Ballistic Missile Defense System (BMDS). This system combines and feeds ground- and sea-based radar data—satellite surveillance too—to the US Command, Control, Battle Management and Communication (C2BMC) system, which provides a top level view of all potential ballistic missile threats.
Anti-ballistic missile defense has come a long way since the 1950s, when the US Navy first installed guided missiles in its fleet. By the 1960s, the Navy began working on a new generation of missile interceptors, eventually creating the Advanced Surface Missile System (ASMS) to better defend against anti-ship fire, in 1964. It was renamed as the Aegis system in 1969. The original Aegis system was developed by RCA (before it was bought by GE) and remained an effective defense until the mid-1980s. It was then that President Reagan authorized the system's further development as part of his Star Wars missile shield scheme. Originally, Reagan wanted to use a gigantor space-based rail gun to shoot down incoming Soviet missiles, but, after someone explained that such a device was ludicrously beyond the available technology of the time, compromised on using the Aegis instead. So the Aegis was integrated into the Lightweight Exo-atmospheric Projectile (LEAP) project eventually developing into the modern Aegis BMD.
The Aegis BMD's pedigree is clear from its components. The system integrates the SPY-1 radar, the MK 41 Vertical Launching System, and the SM-3 Standard missile, controlling them with the ship's on-board C&C system. It can also be integrated into other radar radar systems to expand their effective range and provide a more detailed view of the theater of operations—including even the tracking and downing of ICBMs.
The Aegis system—proven reliable with a record of 23 intercepts in 28 tries—has already been installed on 24 naval warships (5 cruisers and 19 destroyers) with five more getting the system by the end of the year. This increase came at the behest of President Obama in 2009, when he dismantled a ballistic missile shield located in Poland (to appease Russia) and relocated the technology to US ships in the Black Sea. It is also being equipped by numerous US ally fleets—Japan, Australia, Spain, Norway, and South Korea all use the Aegis BMD. [Wikipedia 1, 2 - Navy Live - MDA - Navy - Defense Industry Navy]