Banjo-Tooie devs say the game's darker tone was deliberate

While Banjo-Kazooie was a bright and colorful 3D platformer, the follow-up was a bit more grim. Banjo-Tooie certainly had its bright spots and funny gags, but the overall tone was somewhat darker. That was all by design, according to ex-RARE dev Gregg Mayles. He shared some insight into the darker path in an interview with Nintendo Life.

"It was deliberate. We didn’t want to do the same thing again as the first game and we wanted to surprise players. I don’t think anyone would have expected us to kill off one of the main supporting characters and I can remember us laughing when we plotted Bottles’ downfall. There were some pretty dark and mature elements to the tone that we tried to balance out with our sense of humour, I think my favourite was when Bottles’ family was asking about him and Banjo had to pretend he didn’t know the mole was no more."