This was an April Fools gag. It's playing off of the April Fools strip from 2013
. John isn't a clone... there isn't one on a spaceship with aliens. I really do get people asking me about it all the time though.
One of the more common questions I get is when am I going to bring back the real John...
If you recall John was abducted by aliens while the guys were in Roswell during the trip to look for George's soul... only to be replaced by a clone~!
It would appear that the real John is out of his stasis!