Kyle Katarn, mercenary and former Imperial soldier, has been hired to steal a memory matrix containing the Death Star plans (later retconned as only a set of plans) and invades an Imperial base on the planet Danuta. Initially armed with only his fist and trusty Bryar Pistol, he battles his way through the base's troops and droids — Imperial officers, commandos, stormtroopers, MSE-6-series repair (or "mouse") droids and IT-O Interrogator droids — and acquires an E-11 blaster rifle for his arsenal, ultimately acquiring the plans. Once he retrieves the data, Kyle heads for the roof to board and escape in his ship, the Moldy Crow.
Kyle delivers his set of the plans to the Alliance; they are combined with other stolen data files on the planet Toprawa and beamed aboard Princess Leia's ship, the Tantive IV. The events of A New Hope follow, with the Death Star being destroyed.
Shortly thereafter, General Rohm Mohc reports to Darth Vader for a demonstration of his own new weapon: the Dark Troopers, war droids based on Imperial stormtroopers. In their demonstration, a single squad invades and utterly destroys the Rebellion's Tak base on the planet Talay. Vader is impressed enough to allow General Mohc to continue his project.
The base's destruction leads Mon Mothma to summon Kyle for a meeting. Explaining what she knows about the destruction of Tak Base by the Dark Troopers, she also reveals Crix Madine's role as an Imperial soldier turned Alliance mole in the Empire, and asks Kyle to investigate the Dark Troopers and shut down the project. Kyle agrees, but asks for Jan Ors — the Rebel soldier who revealed the Empire's treachery to him, causing him to defect and become a mercenary — to serve as his mission officer, which Mon Mothma agrees to.
Setting down on Talay (with Jan staying aboard the Moldy Crow and flying it out of range), Kyle infiltrates the base and battles his way through Imperial officers, commandos and stormtroopers to reactivate the local hydro-electric plant and restore power to the base's systems before traveling deeper inside. After tracking down and retrieving a Dark Trooper weapon, Kyle returns to the landing spot so he and Jan can leave Talay.
Analysis of the Dark Trooper weapon reveals its maker, Imperial weapons designer Moff Rebus, who's known to be hiding out in the sewers of Anoat City on the planet Anoat. Jan drops Kyle off, allowing him to head inside. While exploring, Kyle battles Arakyd Industries Viper probe droids, IT-O Interrogator droids, remotes/sentry droids, dianogas and bomb-throwing Grans, and acquires a stash of thermal detonators for himself before locating Moff Rebus at the end of the sewer maze and, after getting picked up by Jan, handing him over to the Alliance for interrogation.
Between Moff Rebus's interrogation and Crix Madine's own information, the Alliance learns that an Imperial weapons site, located on the planet Fest, is doing metallurgical research on new alloys. Kyle is instructed to infiltrate the base and find samples of the metal they're testing, which will give them further clues to the Dark Troopers. Battling his way to the heart of the facility, Kyle retrieves a sample of Phrik metal, defeating stormtroopers, commandos, Imperial officers, remotes/sentry droids, autoturrets and mouse droids in the process before returning to the landing point to rendezvous with Jan and the Crow. Along the way, he picks up an Imperial repeater rifle for his arsenal, and in one of the lowest areas, discovers a cell containing an Ewok.
Analysis of the Phrik metal leads Kyle to Gromas 16, the "blood moon" of the gas giant Gromas, where more Phrik is being mined for the Empire's plans to create armor for the Dark Troopers. Infiltrating the mines and acquiring a Jeron Fusion Cutter — a mining tool used for cutting through rock — which he repurposes as a ranged weapon, Kyle makes his way through Imperial officers, commandos, stormtroopers, probe droids and autoturrets, along with compacting devices, on his way to the mine's reactor core in order to plant a sequencer charge on an exchange coupling, leading into the central power grid. This will destroy the reactor and thus shut down the mines. Planting the charge, however, causes a door to open and Kyle to meet his first Phase I Dark Trooper, a mechanical endoskeleton equipped with a shield and wrist-mounted vibrosword. After destroying it, Kyle escapes back to the surface and boards the Moldy Crow to escape the moon before the mines blow up.
Aboard the Arc Hammer, General Mohc presents a captured Crix Madine to Darth Vader. During their conversation, Mohc reveals that Katarn used to be an Imperial officer but was "weak" and "gave up on the struggle for our new order". He also reveals that he's hired Boba Fett to take Kyle down before he ever gets near the Arc Hammer.
Aboard the Moldy Crow, Jan informs Kyle that Madine has been captured and shipped off to the Imperial Detention Center on the planet Orinackra for termination. The pair head off to rescue him, and after landing outside, Kyle breaks into the Detention Center. Along the way to Madine's cell, Kyle acquires a set of I.M. mines (made by the Imperial Machines corporation) and a Packered mortar gun for his use and has to battle at least one of every regular enemy he's met so far — Imperial officers, commandos, stormtroopers, probe droids, interrogation droids, mouse droids, autoturrets, remotes/sentry droids, Grans and (at one point) a dianoga. Kyle also has to watch out for land mines set throughout the detention center, a precaution against intruders, and at one point must don a gas mask to make his way through an area filled with toxic gas. Ultimately, he locates Madine's cell and frees him.
Madine explains General Mohc's basic history as a decorated soldier of the Clone Wars, his preference for personal combat over technology that separates the warrior from battle, and his role as the mastermind behind the Dark Trooper Project. He also reveals that the Dark Troopers have three phases of construction — mining the Phrik metal on Gromas 16, treating and refining it in a Robotics Facility, and finally constructing the Dark Troopers themselves on the Arc Hammer.
Madine also reveals that an unidentified underworld kingpin is working with Mohc, supplying him with smugglers who can transport the raw materials to the various facilities. He directs Kyle and Jan to the Ramsees Hed Docking Port on the planet Cal-Seti, where Kyle must plant a tracking device on a smuggler's ship that will lead he and Jan to the Robotics Facility. Landing at the Docking Port, Kyle battles his way through Imperial officers, commandos, stormtroopers, Gamorreans, Grans and mouse droids to reach the ship. Kyle also encounters land mines, Power Generating Units (which explode), and another Ewok in a cell. Finally, he plants the tracking device and, though it's not shown, heads back to the Crow.
The smuggler ship's tracking device leads Kyle and Jan to an Imperial facility on the icy planet of Anteevy, where the Phrik metal shipped from Gromas 16 is being refined. Dropped off outside, Kyle picks up a pair of ice cleats to make it easier for him to navigate the more slippery areas before infiltrating the factory. Fighting his way to the core of the factory, Kyle battles Imperial officers, commandos, stormtroopers and autoturrets, plus having to deal with a few crusher points along the way before planting sequencer charges at three thermal power exchange couplings in order to blow up the factory. Kyle also has to acquire another gas mask to deal with the toxins in the air near where the charges need to be placed. After planting the third charge, Kyle faces his first Phase II Dark Trooper; after destroying it and claiming its ammunition, he has to make a final trek through some tunnels and defeat up to three (on the hardest difficulty setting) Phase I Dark Troopers before meeting up with the Moldy Crow again and fleeing the planet.
With the second Imperial facility destroyed, Kyle and Jan travel to the Smuggler's Moon of Nar Shaddaa, their goal being to acquire an Imperial Nava Card with navigation data needed to reach an Imperial Fueling Station where a smuggler's ship will meet up with Darth Vader's flagship, the Executor, and transfer from there to the Arc Hammer. Kyle is warned that General Mohc has placed a sizable bounty and an Imperial death mark on his head; bounty hunters are well known for lurking on Nar Shaddaa, so he must be careful. In spite of this, Kyle overcomes all the Imperial officers, commandos, stormtroopers, remotes/sentry droids, Gamorreans, Grans and Trandoshans (plus land mines and crushers) in his way, acquires a Stouker concussion rifle for his arsenal, successfully retrieves the Nava Card and, with Jan, leaves the moon.
On their way off Nar Shaddaa, Kyle and Jan are captured by Jabba the Hutt's space cruiser, the Star Jewel. Jabba is not aboard himself, instead communicating via a holographic transmission and revealing himself as the crime boss who's been collaborating with General Mohc. Irritated with Kyle's interference in their business, Jabba orders Kyle thrown into a pit to be fed to the Hutt's favorite kell dragon.
In the execution pit, Kyle faces and kills the kell dragon barehanded, and then makes his way into another kell dragon-infested room. Battling his way through the beasts, and traversing the ship, Kyle ends up facing up to ten (on the hardest difficulty setting, counting the first one Jabba ordered him fed to) kell dragons, along with Gamorreans, Grans, Trandoshans and dianogas, plus land mines. In the process, he's able to retrieve his gear and the confiscated Nava Card before rescuing Jan from her cell.
Having re-boarded the Moldy Crow and broken free from Jabba's ship, Kyle and Jan head to Coruscant, the Imperial capital. There, Kyle battles his way through an army of Imperial officers, commandos, stormtroopers, probe droids, autoturrets, interrogator droids and mouse droids, and up to one Phase I Dark Trooper and two Phase II Dark Troopers to reach the Imperial Security Operations Building and its central computer, where the Nava Card can be decoded and its contents transferred onto a data tape. During the mission, Kyle acquires a Dark Trooper's assault rifle for himself, marking his tenth and last new weapon; after decoding the Nava Card and picking up the tape, he gets a message from Jan that she's in trouble, but it's cut off before he can get details. Quickly making his way back to the landing pad, Kyle is confronted by Boba Fett and has to knock him unconscious before Jan and the Crow can land again, having had to deal with a group of TIE Fighters. Navigation data in hand, Kyle boards his ship and he and Jan head off into space.
With the information from the decoded Nava Card, Kyle and Jan head for an Imperial fuel station. There, Kyle fights his way through the station, facing Imperial officers, commandos, stormtroopers, mouse droids, Grans, Gamorreans and Trandoshans, along with encountering Power Generating Units and land mines, and ultimately stowing away in the cargo area of a smuggler's ship. Here, after he and Jan say their goodbyes (as Jan cannot go with him any further), the two part company and the smuggler's ship heads into hyperspace to meet up with the Executor.
When the smuggler's ship lands aboard the Executor, Kyle departs and battles his way through portions of the Super Star Destroyer as it heads towards its rendezvous with the Arc Hammer, taking down Imperial officers, commandos, stormtroopers, mouse droids, interrogator droids and probe droids, along with encountering a pair of land mines, and ultimately up to three Phase II Dark Troopers and a lone Phase I Dark Trooper. He then gets a smaller cargo ship into place for departure to the Arc Hammer. Stowing away on the cargo ship, Kyle heads for his ultimate destination.
Departing the cargo ship, Kyle travels through the Arc Hammer, facing Imperial officers, commandos, stormtroopers, mouse droids, interrogator droids, autoturrets and a handful of QS100 Welding Arms. Kyle also encounters Power Generating Units, crushers and land mines on his way to planting sequencer charges on three power exchange couplings in order to destroy the ship and end the Dark Trooper Project once and for all. Throughout his mission, Kyle also battles up to nine Phase II Dark Troopers and nine Phase I Dark Troopers.
After planting the third charge, Kyle heads for the shuttle bay, dealing with a last group of Phase II Dark Troopers in the process before being confronted by General Mohc himself, controlling a prototype Phase III Dark Trooper — like the earlier models, it can operate independently, but can also serve as an armored and powered exosuit worn by a living soldier, as General Mohc has done. After taking down Mohc, Kyle heads into the shuttle bay, eliminating a final Imperial Officer and seizing control of the Lambda-class T-4a shuttle waiting there. As he flies away from the exploding Arc Hammer, Darth Vader watches from the Executor, noting that this is an unfortunate setback and that the Force is strong with Kyle.
Upon returning to the Rebel fleet, Kyle is awarded the Star of Alderaan for his valor by Mon Mothma herself. Afterward, he reclaims the Moldy Crow and flies off on his own.
