The Great Leader is the former leader of the World Government Organisation. He was the one who ruled the world from the shadows, giving direct orders to Mr. J, Mr. A and Mr. S. After the Pirate, Ninja, and BPM overthrew the WGO in Pirate vs. Ninja 3, he revealed himself as the Scientist, and swore to return. His motives have not yet been revealed.
When adressing the council they only heard his voice. This is why nobody would have guesed him to be the shy and clumpsy Scientist. The character is played by Sjo.