Since no one is really playing the game, I’ll accept my own challenge.
Okay, Season Seven starts and "Fallen/Homecoming" are basically the same, but with Jonas deciding that he needs to remain with Stargate Command. At that point, Jonas remains a part of SG-1.
Daniel becomes SGC-bound while he regains his memories and works towards finding the “Lost City.” Despite this, Daniel occasional joins SG-1 on missions (such as in “Lifeboat” – which was a great Daniel episode; and “Enemy Mine”) for various reasons. The SGC-based episodes (such as “Fragile Balance” and “Chimera”) Daniel will play a role. By the time we get to “Evolution” and Janet’s death, Daniel feels that he needs to be back out there in the field.
Meanwhile, Jonas continues to be his happy-go-lucky self. Jack begins to warm up to him, shown by his playful hazing towards Jonas. Carter continues her “older sister” relationship with Jonas. For his plot arc, like
Hermiod suggested, Anubis takes an interest in Jonas’s unique physiology and uses his research to make with eventually becomes the Kull warriors (although, I wouldn’t make them clones of Jonas). Jonas feels responsible and has a new reason to be out there fighting. In place of the events of "Fall Out", have an episode where the Kull Warriors attack Jonas’s home world, which makes Jonas feel guiltier. This could be a way to take away some of Jonas innocence. Also, for some reason, I can see Jonas coming with Carter on the “Space Race” mission.
In “Lost City” the entire team is out there on the planet where Jack gets his mind zapped (Daniel can be still researching for the Atlantis and SG-1 was the escort).
In season 8, we would have found Atlantis, Jack becomes a general, and Carter is promoted to SG-1 team leader. At this time, Daniel returns to SG-1, making it again a 4-person team, probably under the orders of Jack (at least that can be used to explain away how silly it might seem that a military unit has only 1 officer in it). Much of what happens to Daniel would be the same, now that he is a part of SG-1 again.
In “Lockdown,” Anubis is hell bent on leaving the SGC in Jonas body due to his physiology (same ending as in episode happens). I can also see Jonas trying to seek an apartment like Teal’c, but not being given clearance yet (maybe done more as a throwaway joke in “Affinity” than anything else – perhaps Jonas wants to be Teal’c’s roommate, much to Teal’c’s displeasure). By the time we get to “Reckoning”, Jonas is with Sam decoding the Ancient device on Dakara. In “Threads,” with the galaxy now safe, Jonas must struggle with the decision on whether or not to go back to his home world or stay on Earth, given his actions and indirect responsibility for having his home world attacked (twice) by Anubis and his Kull Warriors. By the end, he would learn that his fears were wrong as he is welcomed back as a hero. “Mobius” would be tricky, as he would disappear for a good portion of time during the alt-timeline part. Maybe have him appear as a host to a system lord or something, but also making him survive with Daniel in the past.
I don’t know how I would work Jonas into seasons 9 or 10. Perhaps he could just be written out of the series by saying that he is helping rebuild his world. Maybe he can pop in for the occasional guest spot. Or, if he had to continue on, maybe have his homeworld completely obliterated by the Ori (with only a handful of survivors, including Jonas, escaping to Earth). Jonas can rejoin Stargate Command at that point, but not necessarily have him as a member of SG-1.
Just my thoughts.
