Had to split this up, because it was too long. Whoops.
I strongly believe that Elizabeth did what she did on the Replicator planet because she was in a position in which she was capable of doing something to save her team and her city. She is not much different from John, Rodney, and the rest of her senior staff in that she will do whatever it takes to protect her people. Having active nanites in her system does add ambiguity to the situation, simply because her nanites have affected her on a very personal, emotional level, and however strong she is mentally, she was clearly very deeply affected when she was made to believe that two entire years of her life in Atlantis were only a fabrication in her mind. As a result, I have considered the possibility that part of the reason that Elizabeth didn't want to return to Atlantis was that she didn't want to live depending on something that forced her through a very difficult emotional experience. However, regardless of her own personal emotional connection to her nanites, I believe that in the very desperate circumstances that her team and her city was in, Elizabeth took the bullet because something more pressing than her individual needs and wants demanded her to make that sacrifice, and she is willing to do so again in "Primum Movens," not wanting to return to Atlantis because she didn't want to put her city at risk. Her sense of responsibility toward her city was so great, and she never would have wanted to return to Atlantis for the simple reason that she possessed something so immeasurably dangerous in her body.
All this makes me wonder, now that Elizabeth is back home, how her personal feelings and beliefs will be resolved. I agree that it would be intriguing to watch her internal struggles as she grapples with the reality that she still has nanites in her system, even though they have been rendered inert thanks to Rodney's anti-Replicator watch. But the nanites are malicious little robots, and even though there are no more Replicators out there in the Pegasus Galaxy, at least those of which we know, I have a feeling that not all remnants of them are truly gone. I feel like what John says here when he went back for Elizabeth foreshadows something darker for future episodes: "It’ll never be over... Getting rid of you and this place doesn’t wipe the slate clean. Who knows what’s still out there?... [That Replicator (Franibeth)] proves there’s no knowing whether they’ll ever be gone." I'm interested in what dangers still lie in the future for our characters and how they will come to face them and deal with their personal feelings and beliefs in the midst of these unending threats. And of course, now that Kate Heightmeyer is also back, I agree that future episodes showcasing the characters' psychological conflicts would provide her with great opportunities to make appearances and help our characters through their personal struggles.
Finally, I also agree that it would be interesting to see John and Elizabeth have a conversation about what happened on the Replicator planet over two years ago. We never saw them talk about it on-screen, and I feel that this subject is going to come up at some point, especially when the loss of Elizabeth impacted John as deeply as it did. On one hand, I don't think that John would bring up the subject himself, and Elizabeth might also not unnecessarily initiate that conversation herself. However, if Elizabeth is asked by those in higher authoritative positions, such as those in the IOA, about what happened to her on the Replicator planet, then this subject might inadvertently give way to a one-on-one conversation between John and Elizabeth about what happened on that fateful day. I think that it'd be important to see them both confront this subject, because even though it could be left to rest in the past, the consequences of that day were far too devastating to be simply forgotten the day after Elizabeth comes home.
Originally posted by PearlofAtlantis1976
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All this makes me wonder, now that Elizabeth is back home, how her personal feelings and beliefs will be resolved. I agree that it would be intriguing to watch her internal struggles as she grapples with the reality that she still has nanites in her system, even though they have been rendered inert thanks to Rodney's anti-Replicator watch. But the nanites are malicious little robots, and even though there are no more Replicators out there in the Pegasus Galaxy, at least those of which we know, I have a feeling that not all remnants of them are truly gone. I feel like what John says here when he went back for Elizabeth foreshadows something darker for future episodes: "It’ll never be over... Getting rid of you and this place doesn’t wipe the slate clean. Who knows what’s still out there?... [That Replicator (Franibeth)] proves there’s no knowing whether they’ll ever be gone." I'm interested in what dangers still lie in the future for our characters and how they will come to face them and deal with their personal feelings and beliefs in the midst of these unending threats. And of course, now that Kate Heightmeyer is also back, I agree that future episodes showcasing the characters' psychological conflicts would provide her with great opportunities to make appearances and help our characters through their personal struggles.
Finally, I also agree that it would be interesting to see John and Elizabeth have a conversation about what happened on the Replicator planet over two years ago. We never saw them talk about it on-screen, and I feel that this subject is going to come up at some point, especially when the loss of Elizabeth impacted John as deeply as it did. On one hand, I don't think that John would bring up the subject himself, and Elizabeth might also not unnecessarily initiate that conversation herself. However, if Elizabeth is asked by those in higher authoritative positions, such as those in the IOA, about what happened to her on the Replicator planet, then this subject might inadvertently give way to a one-on-one conversation between John and Elizabeth about what happened on that fateful day. I think that it'd be important to see them both confront this subject, because even though it could be left to rest in the past, the consequences of that day were far too devastating to be simply forgotten the day after Elizabeth comes home.
Not to mention that the ones that might not have read it yet, might be sort of curious after reading our discussions so openly and might want to find out what Atlantis Rising actually is. Please note that our intentions are the best, we want people to get more interested in this project, hence why we decided to start discussing it more vividly on the last few days. But okay, I will try to be more careful from now on and will try to use spoilers tags more often, if that makes you feel better. 
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