How do you fly bowser's inside story?

after awhile you can get out through the pipe spot.but first you have to help the moles with bowser

You get hit by a laser. then you fall down and the pipe yard inside bowser opens up and you get out through a pipe

Unfortunatly, unless part of the storyline, this doesnt happen.

keep hittin him with a hammer and special attacks

You can walk over there, or you can take the purple swirly circle thing and press "Bowser Castle" and you'll be in Bowser's Castle.