Iran Air Flight 655 Main article: Iran Air Flight 655 On 3 July 1988, Vincennes, under the command of Captain Will Rogers III, was on patrol when it was reported that Iranian Revolutionary Guard gun boats had attacked a Pakistani merchant vessel. Vincennes deployed one of her helicopters to investigate. Shortly thereafter Rogers ordered his ship to move off station 50 miles (80 km) to the north. The destroyer flotilla commander ordered Vincennes to return to her original station. Vincennes's helicopter had followed the Revolutionary Guard gunboats into Iranian waters, and while maintaining contact with the boats, came under gunfire from the Iranians.
The helicopter crew reported that they had come under fire and with that report, Rogers turned his ship around and, with the frigate Elmer Montgomery, moved to intercept the gunboats. By doing so, Vincennes crossed into Iranian waters herself. As the US ships approached, the Iranian gunboats maneuvered, in what Rogers claimed was a threatening fashion. Rogers requested permission to fire and permission was granted by command, without knowing that Vincennes had crossed into Iranian waters. Vincennes and Elmer Montgomery commenced fire upon the gunboats at 9:43 a.m., scoring several hits on the gunboats, sinking two and damaging another.
While Vincennes was firing on the Iranian gunboats, confusion reigned aboard the ship as the tracking of aircraft in the area had become muddled, between Vincennes and other U.S. ships, and on Vincennes itself. Crucially, Vincennes misidentified an Iran Air Airbus A300 civilian airliner, Iran Air Flight 655, as an attacking F-14 Tomcat fighter aircraft. The Iran Air Flight 655 was climbing at the time, and her IFF transponder was on the Mode III civilian code rather than on the purely military Mode II, as recorded by Vincennes's own shipboard Aegis Combat System. Vincennes fired two radar-guided missiles and shot down the Iranian civilian airliner over Iranian airspace in the Strait of Hormuz, killing all 290 passengers and crew on board.
The Iranian government has maintained that Vincennes knowingly shot down the civilian aircraft. Iran Air Flight IR655 flew every day out of Bandar Abbas—a civil as well as military airport—on a scheduled passenger flight to Dubai using established air lanes. The Italian navy and another U.S. warship, the frigate Sides, confirmed that the plane was climbing—not diving to attack—at the time of the missile strike. The U.S. radio warnings were only broadcast on 121.5 MHz, not air traffic control frequencies and mistakenly identified the altitude and position of the plane, so the Airbus crew, if they were monitoring "guard," could have misinterpreted the warnings as referring to another aircraft. Captain David Carlson of Sides later said that the destruction of the airliner "marked the horrifying climax to Rogers' aggressiveness".