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.
Though Lyonie was at first hesitant to assist the Mon Calamari in defending their world, Jar Jar insisted the Gungans come to the aid of Senator Amidala. Later, when Lyonie began behaving oddly and turning his people away from the Naboo, Binks suspected that Lyonie might be loco-nuts.
Recognizing that the Jedi could not mobilize an appropriately equipped aquatic clone army in time to save the Mon Calamari, Yoda suggests that they ask the Gungans for assistance. It was Yoda who made the plea to the Gungan Rep Council.
As leader of the Rep Council, Boss Lyonie holds ultimate authority over the Gungan Grand Army. His approval was required to order it into combat at Mon Calamari and also, more disturbingly, to march it against the Naboo capital.