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In the pilot episode for "Stargate: Atlantis" (Rising, Part 1), a major expedition is launched to the Pegasus Galaxy based on information SG-1 found in Atlantis. Daniel Carter provided context for the information, but it was Rodney McKay leading the science teams.

This seems rather odd, given that McKay was previously a civilian advisor brought in from time to time. Under normal circumstances, it would be Samantha Carter leading the science teams for SGC, and she also played a major role in discovering the Antarctica base to begin with.

Teal'c is offworld leading the Jaffa rebellion at this point, but where is Samantha Carter during the events of "Rising, Part 1"?

Note: I realize why this was done for production reasons, but I'm looking for an in-universe answer.

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    Haven't found an answer myself, however the reason for Rodney McKay leading the science teams was that this was not an SGC operation. The Stargate wiki notes it is due to Antarctica being international territory. It was also around the time of increasing international involvement in the Stargate programme, and not long that before the formation of the IOA. – M_the_C Jul 1 '17 at 20:39
  • @M_the_C While a good point, General O'Neill was able to come, so it's not entirely clear why Carter wouldn't have been able to come too. Besides, she might have been around the SGC during the departure of the Atlantis expedition. – Thunderforge Jul 1 '17 at 20:49
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Possibly awarding Cameron Mitchell the Congressional Medal of Honor

In Season 9, episode 1 "Avalon", we see Cameron Mitchell flying during the Battle of Antarctica (previously seen in Season 7's finale "Lost City, Part 2"). After crashing, he has several hazy memories of being in a hospital.

The first one involves his mother at the hospital while it is decorated for Christmas (indicating that the Battle of Antarctica took place in December*). He also has two more memories of a doctor talking with him as well as Daniel Jackson, both of which happened while Christmas decorations are up.

But his next memory is when the hospital was no longer decorated for Christmas, indicating January or later. In this memory, Carter and two other other air force personnel are in full dress.

Carter: The Congressional Medal of Honor is the highest award for valor in action against an enemy force that can be bestowed upon an individual serving in the Armed Services of the United States of America. On behalf of the President…

Unfortunately, it's too blurry to see if Carter has the rank of lieutenant colonel on her dress uniform (which she was promoted to in the Season 8 premiere "New Order").

I'm inclined to think that the Congressional Medal of Honor was awarded in January, instead of a later month, because Mitchell's memories are still hazy, suggesting that he has not had much time to recover from his memories.

Putting this all together, Daniel Jackson visited Cameron Mitchell in December and then in January, Carter gave him the Congressional Medal of Honor. Since "Rising, Part 1" seems to take place shortly after "New Order", my best guess is that Carter left the base to give Cameron Mitchell his award during these events.

The other possibility, which I have no support for, is that Carter was helping at Area 51, as she was during the first episodes of Season 9. Sam's technical expertise would have been invaluable for helping to repair the ships damaged in the Battle of Antarctica, and with the possibility of more Goa'uld attacking, I could imagine an "all hands on deck" situation there.

* This doesn't line up with the episode before the "Lost City" two-parter, "Inauguration", in which a new US president enters office, because that happens on January 20th after each election.

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"Rising, Part 1" takes place at some point between the season eight episodes "New Order Part 2" (in which Elizabeth Weir leaves to join the Atlantis expedition) and "Zero Hour" two episodes later (in which they reveal their ZPM is pretty much dead... the trip to Atlantis is what drained the last of the reserves).

During that time, both Sam and Teal'c are both still active members of SG-1 (he is not away leading the Jaffa rebellion, that takes place a season later), while Jack O'Neil is not because he's in command of the SGC. Jack is therefore free to go on side-tasks like exploring the Antarctic base without impacting the normal operational parameters of SG-1. Daniel is also a member of SG-1, of course, and he's also visiting the Antarctic base, but SG-1 goes on a lot of missions and some of them Daniel is not particularly suited for, so it stands to reason that he might occasionally be called away to do more important work like translating the stuff to find Atlantis, while Sam and Teal'c are still doing their normal SG-1 duties (possibly with support from other teams, just as if Daniel took a vacation day).

Jack likely wanted to invite Sam along but it's hard to justify benching the whole team just to get one more scientist on an expedition with loads of them. Sam is the foremost science expert at the SGC which is the front lines. Her not working directly on the Atlantis project is not as big a loss for them as her not being on-hand to solve one of the weekly Earth-threatening problems that crop up there is for the SGC.

As for the actual moment when they sent the expedition off at the SGC, Carter and Teal'c could easily be there to watch, within the scope of their normal duties (and Sam at least would probably be interested enough to watch the dial-out), but weren't, but the same reasoning might well apply: they were on another mission at the time. Or, given Carter's somewhat antagonistic relationship with McKay, she may have deliberately found an excuse to not be around while he was at the SGC.

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