To unlock the Pokémon Flute, you need to successfully complete the Electrode chain reaction and take a good photo of the Zapdos that appears. The Zapdos will be flying around the newly opened area.
Once you've captured a decent shot of Zapdos, Professor Oak will be impressed by your discovery and reward you with the Pokémon Flute. This item is crucial for waking up sleeping Pokémon and triggering dance animations.