"Water War" marks the beginning of Season Four for the Star Wars: The Clone Wars animated series. It was initially broadcast on September 16, 2011, paired with "Gungan Attack" to create a special one-hour season premiere.
"Following the assassination of Mon Cala's ruler, tensions escalate between the Mon Calamari and the Quarren, who share the ocean planet. To prevent a full-blown civil conflict, the Republic dispatches Padmé Amidala and Anakin Skywalker, unaware that the Separatists are secretly supporting the Quarren. Now, the Jedi must shield Mon Cala's new, young leader, Prince Lee-Char, from an impending assault."
After King Kolina of Mon Cala is murdered, the already fragile peace between the Mon Cala and the Quarren is threatened, specifically regarding whether the king's son, Prince Lee-Char, is too young and unready to maintain the delicate balance between the two groups (a sentiment which Lee-Char himself shares). Riff Tamson, the representative of the Separatists, further inflames the situation, while Padmé Amidala and Anakin Skywalker, dispatched by the Republic to act as mediators, find themselves unable to effectively intervene. The Quarren delegation departs from the Mon Cala council chamber, though their chieftain, Nossor Ri, does express sincere condolences to Lee-Char for the loss of his father before their exit.
Concerned that a civil war between the two species is inevitable, the Jedi High Council sends a contingent of clone troopers specialized in underwater combat, led by Kit Fisto and Ahsoka Tano. Simultaneously, Lee-Char and his military commander, Captain Gial Ackbar, attempt to rally their people. Regrettably, the Quarren had been preparing for war long before the negotiations failed, and they launch a surprise attack, catching the Mon Cala off guard. Anakin and Padmé join the Mon Cala in battle, but the addition of AQ-series battle droids from the Separatists makes the situation dire. Fortunately, the Republic reinforcements arrive, shifting the momentum, but not without significant casualties. During the conflict, Tamson personally leads aggressive attacks against the Prince, who is under Ahsoka's protection. Tamson attempts to assassinate him, deploying aqua droids into the city's tunnel system when Lee-Char seeks refuge there, but Ahsoka successfully destroys them all. After Tamson's repeated attempts to breach the tube sheltering Lee-Char and Ahsoka, the arrival of clone SCUBA troopers prevents Tamson from reaching the vulnerable prince. Following the Republic's intervention, the Separatists and Quarren are compelled to temporarily withdraw from the besieged capital to regroup, granting the Republic and Mon Cala forces an opportunity to devise a new plan.
Later, the Quarren return, now wielding a terrifying secret weapon: Hydroid Medusas, enormous jellyfish cyborgs with electrified tentacles originating from Tamson's home planet of Karkaris. These creatures prove resistant to the Mon Cala's weaponry. Overwhelmed and suffering heavy losses, the Republic forces are forced to retreat to caves located near the city. Meanwhile, Count Dooku instructs Tamson to gather the captured Mon Cala population and force them to work in internment camps, essentially enslaving them. This announcement shocks Ri, who voices his opposition, but his protests are ignored. Back in the caves, Lee-Char begins to lose hope, overwhelmed by the situation and his perceived lack of experience. However, Ackbar and Ahsoka offer encouragement, reminding him that a good leader knows when to retreat, as well as when to fight. This final piece of advice convinces Lee-Char that there is still hope in the ongoing struggle.
According to the official Facebook page for Star Wars: The Clone Wars, the extensive underwater battle, including the involvement of numerous marine creatures, represented a high point in their animation quality, setting new standards.
Captain Ackbar's line, "It's an attack!" was intended as a nod to his iconic line from Return of the Jedi, "It's a trap!"
The design of the Mon-Cala city was deliberately created to evoke the Mon Calamari ships seen in Return of the Jedi; the towers were essentially designed as landed and docked starships.
Lee-Char's name is a reference to Charlie the Tuna, the mascot for StarKist Tuna.
Kit Fisto's gunship artwork showcased a caricature of him on a cartoon bomb's warhead, accompanied by Aurebesh text reading "Service with a Smile," referencing his famous grin from Attack of the Clones.