Ok, I will try to sum up the 2nd episode, I may be missing something.
JD went out with the surgeon, they went horseback riding bareback on the beach, she loved it but he ended up hurting himself, down there if you know what I mean. She examined him right there on the beach. Later they show them sitting on a sofa joking how she got to third base. They were just about to kiss when Elliot came in interrupting the moment. He later went to ask her out again when Elliot said they had tickets to a Neil Diamond concert.
There was a baby shower for Carla and Turk at the hospital. Everyone playing games and eating. Dr. Cox and Jordan brought in a huge pile of gifts, they gave them all of their baby things and joked that it was their turn to suffer.
Later on, Dr. Cox and Jordan are at home and she tells him that she has been feeling sick for two weeks. They both look shocked and she runs to take a pregnancy test. She is pregnant again. They announce it to the hospital staff. Carla and Turk take all the baby stuff back to their house since they will be needing it again. Since he was suppose to have had a vascectomy and it didn't work, Dr. Cox and Jordan duck tape the doctor to his chair and have the barber shop quartet of the hospital sing "I want my baby back baby back" song from the Chilli's commercial but just sing I want my baby back baby back over and over again to torture the doctor because they never say the word "ribs".
JD is at home alone and the lady surgeon comes by. Elliot tells him that she will take her boyfriend to the Neil Diamond concert. JD and the doc are sitting on the porch staring at the stars and then start making out.
Later, they show JD showing up at the docs house with flowers, he tells her that it has been 2 1/2 weeks and it is time for their 3rd date. She tells him that she is pregnant

and the show ends.
Now they really never show that JD and the doc messed around, so I don't know if the baby is his or not. Can you imagine him being a daddy?