As war continues to fracture the galaxy, planets become pawns in a dangerous chess game. One planet in peril is Naboo, where suffering and civil unrest threaten once friendly relations between the people on the surface and the underwater-dwelling Gungans. Rumors that the Gungans plan to aid the Separatists in an attack on Theed force Senator Padmé Amidala home accompanied by Jedi General Anakin Skywalker.

Arriving on Naboo, Anakin and Padmé meet Jar Jar Binks aboard a bongo submarine at Lake Paonga, the body of water that leads to Otoh Gunga, the hidden Gungan city. Jar Jar confirms that Boss Lyonie has been calling for a Gungan march on Theed. Recently, Lyonie has been giving fiery speeches blaming the Naboo for the Gungans' problems.

Standing before the Rep Council at Otoh Gunga, Boss Lyonie speaks to the assembled officers of the Gungan Grand Army. Lyonie demands that the Gungans take back their world from the overbearing Naboo. Lyonie's aid, Rish Loo, grins with agreement. When the Gungan soldiers leave, Padmé and Anakin speak with the boss.

Lyonie won't listen to Padmé's request to call off his warriors. Though Lyonie claims he speaks from enlightenment, he behaves as if he is under some sort of mental spell. Anakin recognizes something odd about Lyonie's necklace, and uses the Force to pull it off the Gungan's neck and into his hand. Lyonie comes to his senses, as if awakening from a dream.

Lyonie reveals the necklace was given to him by Minister Rish Loo, a Gungan rumored to know ancient mystical powers. In his private offices, Rish Loo contacts Count Dooku and reports on his progress of creating turmoil on Naboo. Loo is paving the way for a Separatist invasion of the planet, in return for a place of power in Dooku's new order.

Boss Lyonie confronts Minister Loo, demanding an explanation, and declaring himself free of Loo's mind powers. But Minister Loo carries his own mind-altering necklace. He activates it, once again casting the boss under his spell.

Anakin senses a disturbance in the Force, and comes rushing into Rish Loo's office. At the minister's orders, commando droids suddenly drop from the ceiling, ready to protect him. Anakin and Padmé hold off the droid attackers while Lyonie grapples Rish Loo.

Loo pulls out a knife and stabs the Gungan boss. With the commando droids distracting Padmé and Anakin, Loo runs for it, shoving his way into a submarine pen and stealing a Gungan bongo. Anakin arrives too late, in time to see the treacherous minister depart.

Boss Lyonie is rushed to a medical bubble. Bandages stop the bleeding, but he has fallen unconscious. He never had time to call off the invasion, and the Gungans are poised to march on the capital. It's up to Jar Jar to convince the Grand Army to stand down.

Jar Jar doesn't think the proud warriors of the army would listen to him. But then, Anakin and Padmé notice that Jar Jar is the spitting image of Boss Lyonie. Anakin tells Jar Jar to take the boss's place, and address the army.

At the swamp surface, Rish Loo has rallied the Gungans, breaking the tragic news of Boss Lyonie's death. Loo urges them to carry out Lyonie's dying command to join with the Separatist army in a march on Theed. At Anakin's prodding, "Boss Lyonie" emerges from the swamps. It's Jar Jar disguised in the boss' robes. The Gungan soldiers are shocked at his appearance.

As Lyonie, Jar Jar addresses the troops. He cancels the attack, calling it a terrible mistake. Jar Jar blames Rish Loo for misinforming the Gungans. With the tables turned against him, Rish Loo flees, jumping onto a waiting speeder bike. Anakin chases after him atop a swift-footed kaadu.

On schedule, Separatist landing ships set down in the plains. General Grievous' invasion force has arrived, and he demands to speak to Boss Lyonie about the cancelled attack. Jar Jar agrees to meet with Grievous aboard his landing ship, with General Tarpals at his side.

An enraged and impatient Grievous yells at the disguised Gungan. Grievous is angered by Boss Lyonie's sudden change in plans. Grievous intends to attack the Naboo with or without the help of the Gungan Grand Army. Jar Jar surreptitiously signals General Tarpals to prepare his troops to resist the droid army.

Tarpals excuses himself from the meeting, and contacts Senator Amidala. He informs her that Grievous is on Naboo, and that Anakin is off chasing Rish Loo. Amidala orders Tarpals to find a way to capture Grievous.

No longer able to stall Grievous, Jar Jar leaves the landing ship conference room in a rush. The angry cyborg charges out after him, only to find that his droid army has been deactivated by his erstwhile Gungan allies. General Tarpals and his troops stand ready to attack.

Grievous scoffs at the Gungans. He ignites his lightsabers, and goads the amphibians into battle. General Tarpals closes in on Grievous, armed with an electropole. Grievous impales Tarpals with a lightsaber, but with his dying breath, Tarpals jams the spear right through Grievous' metal shell.

Inspired by Tarpals' sacrifice, the other Gungans hurl boomers at Grievous' immobile form. The electrified plasma shorts out his circuits. Grievous is defeated!

In a secret headquarters hidden inside ancient Naboo ruins, Count Dooku receives orders from Darth Sidious. The Sith Lord demands that Dooku find a way to release Grievous, for the cyborg warrior is integral to Sidious' master plan for the Clone Wars. Sidious tells Dooku to lure Skywalker into a trap, capture the Jedi, and exchange him for Grievous. Sidious is certain Senator Amidala will agree to release Grievous under such circumstances.

At Dooku's command, Rish Loo lures Anakin into the temple hideout. Finished with the traitorous Gungan minister, Dooku kills Rish Loo, and engages in an uneven duel with Skywalker, overpowering the Jedi with aid from his bodyguard droids.

Dooku contacts Padmé Amidala, demanding the exchange of Grievous for Skywalker. Padmé cannot make the decision easily -- Grievous is a valuable prisoner, and his capture could end the war. But she cannot abandon Anakin. Jar Jar and a recovered Boss Lyonie support this decision.

An hour later, a shackled General Grievous is exchanged for an unconscious Anakin. With that, the Separatists depart from Naboo. Boss Lyonie and Queen Neyutnee are grateful to Jar Jar for once again uniting the Naboo people.