The Squadron fought in several engagements around the time that Coruscant was invaded by the Yuuzhan Vong, notably in destroying the blockade around Talfaglio, and later in the Battle of Coruscant. During the failed defense of the New Republic capital, the squadron lost the majority of its starfighters, and both its Skiprays.
After the battle, Luke Skywalker merged the depleted Shockers with Saber Squadron, the other of the Eclipse Squadrons, to form the infamous Twin Suns Squadron which would soon come under the command of Jaina Solo. When the Republic placed most of its experienced pilots in command of new Squadrons, it is possible that a new Shocker Squadron was created, and that this newer form of the Squadron was the Shocker Squadron that took part in later battles of the War.