Looking through the Family Photos, John finds Pictures of his Father, his Grandfather, and even his Great-Grandfather, all with the same man. A beautiful man, looking to be in his mid 30's in all three series' of Pictures. John's Father is dead, he actually killed himself when he was a Baby; and John's Mother, like every woman in his Family, had abandoned him after he was born. John was raised by his Grandfather, his namesake, who's now in an Old Peoples' Home. John quizzes his Grandfather, who tells the story of the man; of Rodney, who had been Lover to every male descendant in their Family, and who he claims was an 'Ancient', whatever that is. He met John's Ancestor, and they fell in love, but Rodney didn't want to deny his Love the Family he craved, even after he was Married and a Father, their affair continued until the day he died, Rodney was that loyal. By this time, his Son was of age, and too fell in love with Rodney, this pattern continued, but John's Father couldn't live without Rodney and had killed himself. John wants to meet Rodney, angry about his Father, but also curious, and meeting him, Rodney isn't what John expected, and he falls in Love with him too, he doesn't want a Family, and Rodney mentions something called 'Ascension'.
The Ancients are still in control of Atlantis, and Sheppard and McKay have asked to return, surprisingly the Ancients are allowing this. It's not exactly the homecoming that they hoped, this is the Ancients' city, and there's not really anything for John and Rodney to do. The Ancients look on Rodney as though he was incompetent, Rodney's knowledge of Atlantis paling in comparison to theirs, and they're dismissive of him. One scientist is different, and Rodney feels an affinity for him. John is feeling even more put out than Rodney, the Ancients are more skilled in flying the Jumpers than he is, but like with Rodney, one Ancient is different, and he sets about teaching John how to fly like he does. Without realising it, both John and Rodney are getting involved with these Ancients, and the Ancients consider these full blown relationships. What John and Rodney don't know is if it's anything that they want, being with men. They only have each other to talk to about it, and ironically, they're the only men each other could ever have imagined being with.
Dr. Weir was killed shortly after arriving in Atlantis, and since it's a Civilian Expedition, McKay is left in charge. This is was out of Rodney's comfort zone, even though Sheppard is in a similar position, now Ranking Military Officer, and that they hardly know each other, Rodney still needs John's help in making this work for all of them.
Sheppard thinks that he's getting forgetful, asking for people in Departments who don't seem to be there, he assumes that it's just to do with crew rotations, and people coming and going on the Daedalus, but when he looks into things, he finds that there are no records of these people ever having been in Atlantis, people from his Life are disappearing, with those around him not remembering them at all. John is trying desperately to remind them, but the rewriting of their memories is eerily familiar, making John doubt himself. What starts with people on the edge of his perspective, moves on to those closest to him, and for each change, those that are left have their versions of history reconfigured to accept it, until one by one, only Sheppard and McKay are left, Rodney with no memory of it ever being any other way. Atlantis is deserted, with just John and Rodney left, and for Rodney, his relationship with John is the only relationship he has ever had, and for John, the only relationship that he has left.
McKay discovers one of the Ancient Communication Devices that Daniel Jackson used to reach the Ori Home Galaxy, but accidentally activates it himself, and his Consciousness is sent into someone there. Dr. Weir knows that if the Ori get a hold of Rodney, learn of Atlantis, or are able to track the signal, that they will begin an invasion of the Pegasus Galaxy as well. Sheppard is elected, well offers, well insists, on using the Device to get Rodney back, with his Gene; he might have more control over the process. Arriving in the Ori Home Galaxy, he finds Rodney, and their relief at finding each other leads to a surprisingly physical manifestation for both of them, as well as a Heresy to the Ori.
John is Ori, and Rodney an Alteran. The Ori despise the Alterans, and they're in the middle of a bitter War, with John and Rodney no being different, they hate each other, but there's something more between them, and although forbidden, they fall in Love. The Alterans are planning to leave the Galaxy, and John must either abandon his people; or Rodney. He leaves with Rodney, joining the Alterans, but he's been bred to despise them, and is distrusted, in case he reveals their New Galaxy's location to the Ori.