The commercials labeled it as the Scrubs finale. Fortunately for us, it's not really the last episode of the series, just the last one that will be broadcast on NBC (the rest will now appear on ABC). This is good news, not just because it means we get one more season of Scrubs, but also because if this were to be the actual end to the show, it would have been a disappointing sendoff to the series.
The episode mixes real life situations with fantasy, with the latter working as a way to explain the former. J.D. and Elliot are trying to find a cure for a patient whose symptoms are not only hard to diagnose, they continue to worsen as time runs out. Dr. Cox uses the situation as a way to tell a story to his son, putting his own spin on an interpretation of the staff while placing them in a sort of Princess Bride setting.
More over at Athens Exchange.