After the assassination of King Kolina of Mon Cala, the fragile peace between the Mon Cala and the Quarren begins to collapse, centering on the argument that the king’s son, Prince Lee-Char is (as he himself feels) too young and inexperienced to maintain the tenuous co-existence between the two races. Riff Tamson, the ambassador of the Separatists, heats up the argument even further, while Padmé Amidala and Anakin Skywalker, sent by the Republic to mediate between the parties, are helpless to intervene. The Quarren leave the Mon Cala council hall, even though the Quarren chieftain Nossor Ri expresses genuine respect for the dead king to Lee-Char before he leaves.

Fearing that a civil war between the two races is imminent, the Jedi High Council dispatches a company of clone troopers equipped for underwater combat under the command of Kit Fisto and Ahsoka Tano, while Lee-Char and his military commander Captain Gial Ackbar try to rally their people. Unfortunately, the Quarren have long since prepared for war, even before the failure of negotiations, and they attack without forewarning, taking the Mon Cala by surprise. Anakin and Padmè fight side by side with the Mon Cala, but with the Separatists’ reinforcements of aqua droids, the battle already seems lost. Fortunately, the Republic reinforcements arrive and the tide is turned, albeit with heavy losses. During the struggle, Tamson himself launches fierce assaults on the Prince, who’s being guarded by Ahsoka, attempting to kill him and dispatching aqua droids into the city’s tube system when Lee-Char seeks its protection, all of whom Ahsoka manages to destroy. After several assaults on the tube containing Lee-Char and Ahsoka by Tamson, the intervention of clone SCUBA troopers prevents Tamson from reaching the helpless prince. In the aftermath of the Republic attack, the Separatists and the Quarren are forced to temporarily retreat the besieged capital and regroup, allowing the Republic and Mon Cala forces time to plan a new strategy.

Soon, the Quarren return, but with a horrible secret weapon: Hydroid Medusaes, gigantic jellyfish cyborgs with electrified tentacles, which prove resistant to the Mon Cala’s hand weapons. Outmatched and their numbers decimated, the Republic forces are forced to retreat to a set of caves near the city. In the meantime, Count Dooku orders Tamson to round up the captive Mon Cala population to work in internment camps, effectively reducing them to slavery, an announcement which startles Ri, and causes him to protest, to no avail. Back in the caves, Lee-Char begins to despair over the situation and his own inexperience, but Ackbar and Ahsoka do their best to encourage him, reminding him that a true leader knows when to retreat, as well as when to attack. This last piece of advice convinces Lee-Char that there’s still hope in the ongoing battle.