David Poyer - The Cruiser [Kindle azw3]

Newly-promoted to Captain, Dan Lenson's first glimpse of his command is of a ship literally high and dry. The USS Savo Island, which carries a classified, never-before-deployed missile defense system, has run aground on an exposed sandbar off Naples. Captain Lenson has to relieve the ship's disgraced skipper and deploy on a secret mission—Operation Stellar Shield—which will take his ship and crew into the dangerous waters bordering the Middle East.
As a climate of war builds between Israel and Iraq, with threats of nuclear and chemical weapons, Dan has to rally Savo Island's demoralized crew, confront a mysterious death on board ship, while learning to operate a complex missile system that has not been battle tested. But when the conflict reaches a climax, Dan is forced to make a decision that may cost hundreds of thousands of innocent lives—or may save them, but at the cost of his ship and his career.