With the help of Kasan Moor's intelligence, the Alliance launched three consecutive attacks on Imperial bases throughout the galaxy. When Rogue Squadron informed Moor that she has been taken prisoner, she offered to defect and provide the Rebel Alliance with intelligence on Imperial targets. Imperial pilot Kasan Moor's TIE fighter was disabled by Gold Squadron during the battle. While disabling Imperial yachts over Gerrard V, the Rebel force encountered the 128th TIE Interceptor Squadron. Soon after, Rogue Squadron is joined by Gold Squadron, a group of Y-wings now led by Crix Madine they are dispatched to the moon of Gerrard V to aid its quest for independence from the Empire. Rogue Squadron, with the help of Han Solo and Chewbacca in the Millennium Falcon, fought off the Empire and escorted Madine safely off the planet. In response, the Empire launches an attack on Corellia, where Madine is hiding, to prevent his departure. Later, the Rebels learn that Imperial officer Crix Madine wishes to defect to the Rebel Alliance. Soon after, Rogue Squadron helps search for the Nonnah and extract its crew on Chorax. The team is then assigned to escort supplies on Barkhesh. Six months after the Battle of Yavin, Rogue Squadron briefly encounters the Empire at the Mos Eisley spaceport on Tatooine. Rogue Squadron, now under the command of Wedge Antilles, continues to fight the Empire to protect the newly formed Republic. After the deaths of Emperor Palpatine and Darth Vader, the Galactic Empire collapsed, but was reborn under a mysterious new leader. Six years after the Battle of Endor, the Rebel Alliance has established the New Republic, which now controls three quarters of the galaxy. As the Empire gathers strength for an all-out assault on the Rebel forces, Luke Skywalker and Wedge Antilles form Rogue Squadron, a group comprising twelve of the most skilled X-wing pilots from the Rebel Alliance. Six months after the Battle of Yavin, the fliers of Rogue Squadron are engaged in a desperate battle for the survival of the Rebellion. Star Wars: Rogue Squadron is set during the war between the Galactic Empire and the Rebel Alliance.

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