My pet theory is that Ba'al is behind it somehow. He is the one Goauld with access to cloning technolgy, and boy he is not afraid to use it. So he probably cloned everyone in Atlantis (got the genetic material through some Trust's agent infiltrated in Atlantis, since he is the Trust leader. Of course, that doesn't explain Summer. Unless he had some ADN from before or is in league with the Wraith. Scary that). My idea is that they are trying to attack the real Atlantis and captured John because without him the plan cannot work. The drug might have screw up with his memories and/or they are using behavioural modification on him. The latest Rodney is the real Rodney, the one before him probably was a clone with a symbiot inside or something similar. This doesn't explain why they don't know about the Athosians.

The other theory (though not the favourite) is that it is all happening inside John's head, in a similar system to the one from Aurora and the Wreith are trying to extract the codes to break in Atlantis from him. Rodney has somehow managed to insert himself in the system like he did before and can change some things and bring in new people like Teyla to help him convince John of the truth. For whatever reason they cannot just tell him, although that's why I find this theory not as satisfactory.

Of course, I'm looking forward to the real story, but speculating about is fun.