It's the eve of the Clone Wars. Count Dooku has made a deal with Sabaoth scientist named Cavik Toth has created a biological weapon that could be used against the Republic. Meanwhile, Adi Galia has been tasked with recruitin the mercenary Nym to aid Republic efforts in the inevitable war with the Separatists. Nym accepts on the condition that Galia helps free some of his men, who have been in a Trade Federation prison for ten years, and help to recapture his base on the planet Lok. Galia agrees, and they free the men.

They discover that the Trade Federation has been creating a weapon called Trihexalon and move to shut down all production by destroying all of its factories. However, several Hex weapons have already been created, and you must now destroy all of them and kill Cavik Toth before they can be used against the Republic in the Battle of Geonosis.

!!This work includes examples of:

* [[AllThereInTheManual All There in the Bonus Level]]: You need to play the unlockable BonusLevel "Jango Fett" to find out why the eponymous bounty hunter wanted to capture Reti. [[spoiler: Reti worked as a mercenary for Race Kartan, a smuggler that Fett took down in a previous mission. The two of them had a run-in when Reti rushed in to defend Race.]]
* AndTheAdventureContinues: [[spoiler: Vana unexpectedly gets a panicked message from Reti, who's apparently on the run from serious trouble. Cue the rest of the Revenants dashing off the save him, their futures uncertain]].
* AwesomeButImpractical: Force shockwave. It takes forever to recharge, and anything you were planning to do with it could be done just as easily with either Force lightning or Force timeslow.
* BigBulkyBomb: The unlockable Advanced version of the ''Havoc'' can charge up one called the Plasma Scourge (which was actually a regular feature in the previous ''Starfighter'' title).
** To a lesser extent, Cruise Missiles, which the ''Havok'' also carries.
* BlackAndWhiteMagic: Averted. Force lightning and Force shockwave are dark side powers, but Adi doesn't mind using them.
* BonusLevel: "Jango Fett", "The Lone Gunship", "Advanced Training", and "X-Wing vs. TIE Fighter".
* CoolStarship: Obviously. There's the Jedi Starfighters themselves, Reti's ship, the ''Zoomer'', Nym's bomber, the ''Havoc'', Jinkins' ''Freefall'', the Mere (as in the dominant sentients of Maramere) Heavy Cruisers (Tritus, Kethor, and two unnamed), the Sabaoth fighters, the Sabaoth Destroyers, and the Hex Deployers.
* DiscOneNuke: Villainous example: Trihexalon is introduced very early.
* TheDragon: Lieutenant Bella is this to Admiral Toth.
* EasterEgg: ''[[VisualPun Literal]]'' Easter Eggs are hidden in Mount Merakan, along with a battle droid building a snowman.
* EvilBrit: Cavik Toth. (Though, given the setting, he's likely an Evil [[FantasyCounterpartCulture Coruscanti]])
* FiveFiveFive The outtakes feature Mace advertising a Jedi Starfighter plane rental with the number 1-555-FLY-JEDI.
* FragileSpeedster: The appropriately-named ''Zoomer''.
* HarderThanHard: The difficulty after hard? Co-operative. Yes, it's going to be so difficult, you need a friend.
* HilariousOuttakes: One of the unlockable extras.
* JackOfAllStats: Adi's eponymous starfighter.
* KillSat: The Orbital Cannons. Two of these have to be destroyed during the assault on Nod Kartha, to allow the ''Kethor'' to take down the shields blocking access to the planet. Nym's forces later salvage one and mount it on Lok's moon to aid in retaking his old base.
* LeadTheTarget: In the training mission, Saesee Tiin teaches this and other basic fighter combat principles.
* LifeEmbellished: The "My Day At Work" unlockable short.
* LoadsAndLoadsOfLoading: It's far from the worst offender, but expect to sit for 45 seconds when you first turn the console on, then another 45 seconds when you select your mission.
* MacrossMissileMassacre: Nym does this with Cluster Missiles once he has them, as do the unlockable Advanced versions of the ''Freefall'' and the ''Zoomer''.
* MightyGlacier: Nym's fighter, the ''Havoc''.
** And the LAAT Gunship. Slower than all other ships save for the ''Havoc,'' but it comes with more health, a stronger shield, several limited missiles, and the rechargeable mini-SPHAT lasers that can reduce many ships to scrap in only a couple of seconds. In fact, it alone can make short work of everything but the endgame capital ships.
* OldSchoolDogfight: The last two bosses are this, although you can nail the first with your KillSat if you're lucky.
* PaletteSwap: The Mercs in the "Jango Fett" bonus level are recycled from the first ''Starfighter'' game, all the way down to the boss, Race Kartan, being a less durable copy of ''Starfighter'''s FinalBoss.
* RammingAlwaysWorks: In the level "Hammer and Anvil", the ''Kethor'' sustains crippling damage from one of the Orbital Cannons in the level's opening cutscene. Later, after you take the cannons out, Captain Orsai (after evacuating his crew) steers the doomed ship into one of the main shield generators, destroying it and opening Nod Kartha up to attack.
* SequelEscalation: Two examples.
** In the first game, all you did was destroy a droid factory and then participate in the Battle of Naboo. In this game, you shut down creation of a biological weapon, hunt down its creators, and then prevent its use in the Battle of Geonosis.
** In the first game, you couldn't damage landers, and there was only one capital ship in the final level. In this game, you destroy a Trade Federation lander in the first level, several over the course of the game, and you encounter and destroy several capital ships, including three in the last level alone.
* ShoutOut: Complete the right secondary and hidden objectives, and you can fly an X-wing, a TIE fighter, or the ''Slave I''.
* StuffBlowingUp
* TheDevTeamThinksOfEverything: One mission features a Saboath Destroyer launching tugs the player must intercept. You may try to destroy it outright, allowing your own tugs to salvage in peace. Cue another Destroyer warping in while the enemy commander laughs maniacally.
* UnskilledButStrong: The unlockable Saboath Fighter. It has no special weapons or any other fancy tricks, but its regular lasers deal double damage and its shields recharge twice as quickly.
* VerbThis: From the third level, after blowing up the second Troop Transport: "Transport ''this''".
* VillainousBreakdown: Cavik Toth experiences this during the final level.
* ZeroEffortBoss: You can kill the FinalBoss by just flying in a circle on the far side of the map and spamming Force lightning.
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