Kyle Katarn infiltrates an Imperial base on the planet Danuta, in order to steal the Death Star plans. The Mission to Danuta results in Rebel possession of the plans that would later be given to Princess Leia and the destruction of the Death Star.
After the Battle of Yavin, Kyle is again contacted by Mon Mothma to investigate an Imperial assault on the Tak Base of Talay, using a type of Imperial trooper never encountered previously. After the attack on Tak Base Kyle infiltrates the ruins of the base and discovers a prototype dark trooper weapon. The initials “M.R.” are discovered on it, which are found to stand for Moff Rebus, an infamous Imperial weapons engineer. This investigation reveals the dark trooper project, led by General Rom Mohc, and this leads Katarn to Anoat, where he finds the Moff hiding in the sewage system of Anoat City.
During interrogation, Moff Rebus reveals the location of a testing facility for the mineral phrik, used in the construction of dark troopers, on the planet Fest. After obtaining a sample of this mineral, Kyle is led to the Gromas system, where phrik is mined and the phase-I dark troopers are manufactured. After the destruction of this facility, Crix Madine is found to have been captured by the Empire and sent to an Imperial detention center on Orinackra. Once Kyle has rescued Madine, he provides Kyle with critical information regarding the dark trooper project.
Kyle travels to the Ramsees Hed docking port on Cal-Seti, which is used for Imperial runs to the frozen planet of Anteevy, where the second phase of dark trooper construction was completed. After smuggling himself aboard an Imperial ship, Kyle reaches Anteevy and destroys the Ice Station Beta facility. He is afterwards led to Nar Shaddaa, where he obtains a Nava card. At this point in the scenario, the Empire has placed a large bounty on his head, and as he pulls out of Nar Shaddaa, the Moldy Crow is captured by Jabba the Hutt in the Star Jewel.
Here, Kyle is stripped of his weapons and has to fight hand-to-hand with a kell dragon. After obtaining his weapons, he and Jan Ors escape to Coruscant, the only place where Kyle can insert the Nava Card into a decoder to reveal data chips used for additional information. On his way to his ship, Kyle finds the Crow missing and Boba Fett (hired by Mohc) waiting for him. He defeats Fett after a hard fight and then travels to the Imperial Fuel Station Ergo, where he sneaks onto the Executor. From here, he smuggles himself aboard the Arc Hammer, where the third and final phase of the dark troopers is being overseen.
Finally, Kyle faces Rom Mohc, spearhead of the operation (who is using the only phase-III dark trooper exoskeleton in existence), and defeats him. Kyle proceeds to blow up the Arc Hammer and escape. Watching from the Executor, Darth Vader comments that this “is an unfortunate setback” and somewhat prophetically notes that “the Force is strong with Katarn.”
For his actions and bravery in the face of defeat, Mon Mothma awards Kyle the Star of Alderaan.