After the destruction of the first Death Star, Darth Vader has begun a new project for the Galactic Empire. Meanwhile, in the Rebel Alliance, rumors have grown concerning "ghost ships" attacking Rebel patrols. Rookie One (acted by Jamison Jones in cut scenes, his voice is provided during the "shoot scenes"), while flying with his wingman on patrol near the planet Dreighton, receives a distress call from a YT-1300 transport, the Corellia Star, which is being attacked by TIE fighters. The pilot has crucial information about the Empire's new project. After fighting off several TIE Fighters, Rookie One's wingman destroyed by one of the unseen attackers, and Rookie One's ship is shot down, but he is able to eject himself before the rest of his ship explodes and crash lands on a planet, where the captured transport had been forced to land. Having survived the crash landing, Rookie One follows a tracking scanner to an Imperial station, where the Corellia Star is being held. After fighting stormtroopers, he finds the transport and its information, but the station's doors close before he can escape, forcing him to fly through mining tunnels. He is able to find another way out and escapes through hyperspace. Back at Pinnacle Base, Admiral Ackbar (digitally copied from Return of the Jedi and inserted into the game) helps the pilots understand the message from the freighter. The Alliance learns that the Empire has constructed a secret mining facility in the asteroid Belt of Arah, somewhere in the Dreighton Nebula, and Rookie One is sent along with a squadron of X-wings to destroy it. Along the way, they encounter derillium minefields and TIE Interceptors. The facility is not simply mining ore, but is supplying rare metals required to manufacture the new V38 "Phantom" TIE, equipped with a cloaking device invented by Grand Admiral Sarn. After the squadron opens a way into the facility's reactor core and destroys it, narrowly escaping the blast, squadron leader Ace Merrick is killed along with wingman Ina Rece by an ambush of Phantom TIEs. Rookie One manages to evade the TIEs and escape. At Pinnacle Base, Admiral Ackbar comes up with a plan for two people to infiltrate the facility building the Phantom V38s at Imdaar Alpha. Rookie One takes a crash course in TIE piloting from Admiral Krane with two TIEs stolen from the Empire. Then, they head out to the jump point where they encounter TIE Interceptors. After defeating them, Rookie One heads to Imdaar Alpha alone and encounters sentry guns and force fields along the way. He meets with Ru Murleen (played by Julie Eccles), Rookie One's previous flight instructor from Rebel Assault. They fly to an Imperial Landing Platform on the far side of a swamp on Speeder Bikes. Disguised as stormtroopers, Rookie One and Ru Murleen steal an Imperial shuttle and board Admiral Sarn's cloaked Super Star Destroyer Terror. After defeating numerous stormtroopers within the Super Star Destroyer and later in the maintenance tunnels, they steal a Phantom TIE from the hangar. After destroying the Terror from inside, along with many other Phantom TIEs, Darth Vader kills Admiral Sarn for his failures and escapes on a TIE interceptor. The Imdaar Alpha facility manufacturing the new fighters suddenly appears on Imdaar's moon, as it was also equipped with a cloaking device that was damaged when the Terror exploded. After destroying the facility and returning to a Rebel base, the leader of the Rebels thanks them for saving the day once again. Darth Vader informs the Emperor of what happened and the stolen Phantom TIE as the Rebel Base self-destructs. There are three endings depending on the difficulty.