This episode was mostly about Eliott and J.D. who are definitely rekindling their friendship going out to dinner and movies together. Basically they're doing everything in a relationship without the sex.  

Dr. Kelso claims to be leaving the hospital Coffee Bucks to go on a vacation with his wife, but J.D. and Elliot run into him at another Coffee Buxks.  We find out he's not taking too kindly to the leisurely life of retirement and misses the action of the hospital.  

Kelso also sits down J.D. and Elliot and they have the most serious conversation they've probably had in the series' history.  They decide to put aside all the drama and think they could make a relationship work.  The episode ends with them going for it and holding hands on their walk out.

The major medical sideplot of this episode is Dr. Cox and Turk's patient, a man, Mr. Halford needs a kidney transplant.  Cox uses Turk as his surgeon, but doesn't trust him, and closely watches over him.  When Mrs Halford's kidney isn't a match, the Tod and and Dr. Cox save the day by finding another couple, the Brinkleys, where the man needs a transplant and his wife's kidney will work for the Halfords and vice versa.

However, there's a dilemna, the Halfords' surgery will be a week after the Brinkleys so the Halfords do not trust the Brinkleys will be around to give him his kidney.  The solve the trust issue by performing the surgery at the same time and Cox and Turk seem to solve their trust issue at the same time.

Additionally, the Janitor has his own little subplot as he weasles his way back into employment.  With Dr. Maddox gone, he tricks the new janitor into thinking he's fired.  His next trick is he just starts showing back up to work and convinced the payroll lady he's still working there... and gets paid twice as much.  Good, we missed the Janitor.