When the greedy Trade Federation invaded Naboo, Panaka and his security forces were outnumbered by the Trade Federation droid army. Two jedi, Qui-Gon Jinn and his apprentice Obi-Wan Kenobi helped the queen to escape from Naboo. After that, the group forced landed on the planet Tatooine for ship repairs. Even in the presence of the Jedi knights, Panaka advices to the queen based on his own point of view of the situation. When the ship was repaired the group travelled to Coruscant, there they met with Chancellor Valorum trying to gain the support of the Galactic Senate for Naboo. Since the negotiations for the support were in vain, the queen decided to travel back to Naboo, and regain control of the planet. Panaka knew this was a dangerous move, however his loyalty to her was unquestionable.

  With the help of the Gungans, the two jedi and a young boy named Anakin, Panaka and his soldiers were succesful on obtaining the freedom for Naboo.