How do you defeat bowser in bowsers 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

If you mean the 2nd battle in toad town, i recommend you use the jump helmet a lot.

When bowser gets huge hit him. The the fawful will come out. When its your turn suck it up and then keep fighting.

I'm not sure what you mean. For the wiggler that is fought after the carrot challenge, you need to punch each body segment until they are all yellow, then attack the head. For durmite, the creature...