Found by
terrycene - it is: The Water Grinds the Stone which part 3 of the Salt on a Wound series by auburn. Thanks so much.
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I can't recall all the details and my search was bust. I believe it was a fairly large story with at least one follow up piece. Near the end of the main story Sheppard was using the Chair in Antarctica to defend the Earth and he ran out of missiles. The bad guys - I'm not certain if they were Wraith or Ori or Goa'uld - brought down the base and Mitchell had Sheppard (injured and trapped in the Chair) beamed out but while it might have saved his life it broke John's neck and he was awake and aware but on life support and really not able to communicate or at least no one seemed to have the time or patience or care to try to communicate wit him. Vala and Teyla make deal with someone I don't know who they get to use of the Goa'uld sarcophagus on John. There was no guarantee it would work since injury was no longer fresh. In the end he returns to Atlantis permanently and as far as TPTB on Earth are concerned John Sheppad is dead. I don't recall what name he took on Atlantis but it was some sort of play on John I think. The follow up story had John with other citizens of Atlantus helping with a harvest and he was suddenly dizzy and terrified that all this was just a dream and he was even then trapped in his body with no ability to do anything or to really communicate.
Any help or pointers would be greatly appreciated. Thanks in advance.

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I can't recall all the details and my search was bust. I believe it was a fairly large story with at least one follow up piece. Near the end of the main story Sheppard was using the Chair in Antarctica to defend the Earth and he ran out of missiles. The bad guys - I'm not certain if they were Wraith or Ori or Goa'uld - brought down the base and Mitchell had Sheppard (injured and trapped in the Chair) beamed out but while it might have saved his life it broke John's neck and he was awake and aware but on life support and really not able to communicate or at least no one seemed to have the time or patience or care to try to communicate wit him. Vala and Teyla make deal with someone I don't know who they get to use of the Goa'uld sarcophagus on John. There was no guarantee it would work since injury was no longer fresh. In the end he returns to Atlantis permanently and as far as TPTB on Earth are concerned John Sheppad is dead. I don't recall what name he took on Atlantis but it was some sort of play on John I think. The follow up story had John with other citizens of Atlantus helping with a harvest and he was suddenly dizzy and terrified that all this was just a dream and he was even then trapped in his body with no ability to do anything or to really communicate.
Any help or pointers would be greatly appreciated. Thanks in advance.