I generally plan a story by have a beginning then have an end; once that happens, I fill in between and make sure that it connects and makes sense
The idea either comes up from creating a character(s) then building a world around them to create a story
After thinking up a character design, I draw the character and then draw them again after some time to change their appearance until they look good
I sometimes make a script for dialogues, but mostly just wing it after thinking about the dialog and going straight into making a panel