Tensions between the Naboo and the Gungans have increased as the Gungan leader, Boss Lyonie, has openly showed Separatist sentiments. Seeking to prevent any type of conflict, Anakin Skywalker, Padmé Amidala, and Jar Jar Binks investigate the Boss to discover that he has been put under a mind control spell by an evil minister. They undo the curse, but not before the minister shoots Boss Lyonie and flees, with Anakin giving chase.
With a dying Boss, Padmé tries to save face by having Jar Jar dress up as the Boss and take his place to keep peace until he recovers. Thankfully, Jar Jar looks like the Boss's twin, so even when Jar Jar shows up at a funeral for the Boss, everyone buys it. Problem is, General Grievous arrives at the funeral to talk with Boss Lyonie about a Separatist invasion of Naboo. Terrified, Jar Jar tells General Tarpals of the Gungan Royal Guard to rally the army to capture Grievous while he stalls for time.
Jar Jar, despite fumbling through the conversation, actually manages to convince Grievous he's Boss Lyonie for a good amount of time before the General figures the ploy out and chases Jar Jar off his ship. The General finds himself surrounded by the entire Gungan Army, who throw every man, spear, and bomb they have at Grievous en masse in an attempt to defeat the living war machine, but none of it works. Grievous drives his lightsaber through General Tarpals and brags about killing the Gungan, only for Tarpals to shove his spear through Grievous' shoulder and give the rest of the army the opportunity to break Grievous down and capture him.
Meanwhile, Anakin hunts down the evil minister who brainwashed Boss Lyonie, arriving just in time to see Count Dooku impale him. Dooku explains that the Separatists want to retake Naboo since it was where the Sith started the war, after all, and insults Anakin again for not realizing the Sith's control over the conflict. The two duel, with four MagnaGuards helping Dooku, until the Count lifts Anakin into the air and electrocutes him into submission. This gives Dooku all the leverage he needs to arrange for Grievous' return, while exchanging Anakin's freedom in return. War has been averted, but the Separatist threat lives on, and a hero is dead.
- Arc Welding: Dooku's comments make it clear that he was with the Sith even during the events of The Phantom Menace, ten years before he publicly became known as a Sith Lord.
- Emergency Impersonation: Jar Jar is forced to dress up as Boss Lyonie in order to stop the Gungan Grand Army from marching on Theed, which was ordered by the mind-controlled Boss.
- Hypno Trinket: Rish Loo's talisman forces Boss Lyonie to conspire with General Grievous to plan an attack on Naboo.
- Oh, Crap!: Jar Jar's entirely justified reaction upon seeing General Grievous.
- Prisoner Exchange: Dooku forces Padmé to give up General Grievous to the Separatists by torturing Anakin and threatening to kill him. Even though Grievous' capture likely means the end of the war, Padmé loves Anakin too much to see him killed because of her.
- Senseless Sacrifice: General Tarpals sacrifices himself so the Gungan army can capture Grievous. Unfortunately, the Republic is forced to exchange him for a captured Anakin Skywalker, rendering Tarpals' death pointless.
- You Have Outlived Your Usefulness: Dooku murders Rish Loo after the Gungan lures Anakin to his laboratory.