In the sixth season, J.D. deals with the news that he's going to be a father, Dr. Cox worries about how his anger is going to affect his offspring, and The Janitor wonders whether his personal vendetta against J.D. is a waste of time. Also, Elliot decides she too wants children.
The wackiness reached an obvious limit late in that year, and when the writers tried to dial it back last season, J.D. was no longer a recognizable human being who could work in more down-to-earth stories.