A group of pirate repulsortanks was sent out to recover the spice, and Jar Jar was taken prisoner aboard one of the tanks. Jar Jar clumsily bumped into a Weequay driver, sending the tank skidding askew and slamming into another vehicle. Taking advantage of this distraction, the clones charged against the tanks. The pirates blasted the tank Jar Jar was on, sending the Gungan flying, but the clones rushed in to take the Weequays prisoner.

Investigating a new battle droid presence on Naboo, Padmé Amidala and Jar Jar Binks stumbled on a Separatist plot to hatch the Blue Shadow Virus, a deadly plague wiped from the galaxy generations ago. With the help of Anakin, Obi-Wan, Ahsoka, and several clones, the plot was foiled and the diabolical mastermind behind the Separatist plot -- Dr. Nuvo Vindi -- was captured.

With Republic forces bogged down in the fight for Mon Cala, Yoda turned to the Gungans for help. Jar Jar convinced his fellow Gungans to come to the aid of Padmé and the Mon Calamari people.

The Gungans prepared an army and arrived at Mon Cala on a Republic cruiser, diving into the planet’s seas to confront the Separatists. But Jar Jar was captured – along with Anakin and Padmé – in a Separatist counterattack.

After the shark-toothed Separatist warlord Riff Tamson bit a hole in Padmé’s helmet, Jar Jar saved his old friend from drowning with a well-aimed loogie – a bit of “Gungan waterproofin’.”

Following the Battle of Mon Cala, the Republic received disturbing reports that the Gungans planned to join the Separatists in an attack on Naboo’s capital of Theed. Anakin and Padmé met with Jar Jar, who confirmed that Boss Lyonie had been blaming the Gungans’ problems on the Naboo.

Anakin discovered that Lyonie’s aide, Rish Loo, was manipulating the Gungan boss through a strange necklace. With his plot revealed, Loo stabbed Boss Lyonie and fled Otoh Gunga.

While Boss Lyonie recovered from his injuries, Jar Jar took advantage of his strong resemblance to the Gungan leader, donning Lyonie’s ceremonial garments to address the Gungan army.

Jar Jar cancelled the attack on Theed, calling it a terrible mistake and denouncing Loo – who once again fled before he could be apprehended. When General Grievous arrived to lead the Gungan army, he found himself fighting the Gungans instead.

When Bardotta’s Queen Julia contacted the Republic for help investigating the mysterious disappearance of her planet’s spiritual leaders, she had a special request for Supreme Chancellor Palpatine: send Jar Jar Binks as an ambassador. The Republic agreed, but insisted on sending Mace Windu as well. That angered the Bardottans, who distrusted the Jedi Order.

Julia greeted her old friend joyously, eager to rekindle their romance, but then told him she had discovered a terrible plot directed at the planet’s Dagoyan Masters. While Jar Jar and Mace discussed the Republic mission, the queen disappeared.

Julia’s ministers told Jar jar and Mace that a secret cult on Bardotta was seeking to plunge the galaxy into darkness. Trying to rescue the queen, Jar Jar and Mace got separated, and the Gungan was attacked by a masked figure who blew dust into his face. The dust made Jar Jar vanish.

When the spell faded, Jar Jar found himself a captive of the Frangawl cult, imprisoned along with Queen Julia. Mace Windu arrived to save the queen, and he and Jar Jar battled the cultists. But the Frangawl adepts spirited Julia into a starship and fled.

Jar Jar and Mace tracked Julia’s captors to Zardossa Stix, where the Frangawl cult planned to transfer the living Force from the queen to their mysterious Great Mother. The Gungan and Jedi had to fight cultists and savage gundarks sent to stop them.

The Frangawl cult’s Great Mother was the Nightsister matriarch Mother Talzin, who had learned a secret ritual that could make her the most powerful being in the galaxy. Mace and Jar Jar raced across the desert to the Temple of Malmourral, hoping to save Julia and stop Talzin.

In the nick of time, Mace and Jar Jar foiled the Frangawl plot, ruining Talzin’s plans. Jar Jar and Julia were reunited, and the Bardottan queen looked forward to a new beginning for her people and the Jedi.

After Padmé Amidala's tragic death giving birth to twins Luke and Leia on Polis Massa, Jar Jar joined her funeral procession on Naboo, their shared homeworld.