When the king of Mon Cala is assassinated, talks break down between the Mon Calamari people and the Quarren, co-inhabitants of the aquatic world. To stop a civil war, the Republic sends Padmé Amidala and Anakin Skywalker, but unbeknownst to them, the Quarren are already being backed by the Separatists. Now the Jedi must protect Mon Cala's new leader, the young Prince Lee-Char, from the attack.

Anakin Skywalker and the rest of his Jedi team have been overrun by the Separatist surprise attacks led by Riff Tamson while Prince Lee-Char and Ahsoka must evade capture on their own. Unable to summon more Republic aid, Yoda calls upon the help of the powerful and amphibious Gungan Grand Army, but whether they will be enough to stop the Separatist siege is uncertain. An incensed Tamson doubles his efforts in tracking down Prince Lee-Char, unleashing the reinforcements given to him by Count Dooku in an assault that churns the oceans.

The Republic and Gungan forces have been captured by Riff Tamson and his Karkarodon enforcers. Now, it is up to Ahsoka and the young Prince Lee-Char to unite the fractured people of Mon Cala and drive out the Separatist invaders.