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During the Clone Wars, Boss Lyonie served as the local leader of the Gungans of Naboo, chairing the Rep Council in Otoh Gunga. When the Republic needed reinforcements to prevent the Separatist takeover of Mon Cala, the Jedi Council asked Boss Lyonie to send in the Gungan Grand Army. Jar Jar Binks was quick to insist the Gungans help, especially since their loyal ally Senator Amidala was endangered.
Though Lyonie proved a boon to the Republic during that campaign, a sudden tide of unrest among the Gungans against the Naboo caused many to fear that he would be siding with the Separatists.