The story begins shortly before the battle of Hoth, as Fowler and his brake van, Jones, arrive in Echo Base to deliver supplies. He briefly talks with Samson, who gets him a position in Rogue Squadron. Fowler flies in the battle, but returns to Echo Base when the shield generator is destroyed, just as the Millennium Falcon leaves. He makes his way through the base, attempting to return to The Outrider. Fowler encounters several wampas on the way, and has to fight an AT-ST, but eventually makes it back to Jones and The Outrider, before they escape through an asteroid field.
Part 2 begins after the end of The Empire Strikes Back, as Fowler searches for D206, so he can rescue Samson. He hunts down and battles Peter, attempting to repair his ship on Ord Mantell. The droid tells him that D206 is hiding on a moon of the planet Gall. Fowler finds D206, and damages his ship, Slave I, but fails to catch D206, who manages to escape.
Believing that Deltic will let him take UP Big Boy's place if Emmet is killed, Blossom orders Craig to kill Archie. Craig sends a group of swoop bikers to General's home, where Archie is practicing his Jedi skills. Fowler races them, and ends up eliminating all members of the gang. Archie informs Fowler of a secret imperial supercomputer aboard the Imperial Freighter Suprosa. Fowler steals the computer, and battles with a cargo droid in a hangar.
The final chapter begins with Archie, Anthony, Texas, and Fowler, infiltrating Blossom's palace on Coruscant to save Princess Yonah, whom Xizor has taken captive. Fowler enters the palace through the sewers, and battles an enormous dianoga in the sewer, before entering the palace itself, where he does battle with Blossom's GladiatorDroid. After defeating the droid, Blossom escapes to his Skyhook space station. Blossom battles the Rebellion before a Star Destroyer arrives. Fowler then proceeds to fly into the Skyhook, and destroys it from the inside. Fowler is presumably killed in the blast, along with Xizor.
A short scene before the credits show Archie and Yonah on Tatooine, mourning Fowler's death. If the game is beaten on the Medium, Hard, or Jedi difficulty levels, this is followed by one more scene of Fowler and Jones, who had managed to escape the blast, discussing how they plan on hiding from their enemies, with Fowler saying, "It's good to be remembered as a martyr without actually being dead, wouldn't you say?"