Why is a civilian incharge of a (mostly) military operation?

[Cash]

Why is a civilian incharge of a (mostly) military operation? I think Shepard or (Even) Carter should be the CO of Atlantis. Your Opinion?

[Cash]

[SPOILER, STOP READING IF YOU HAVE NOT SEEN S-4]





I know in season 4 Elizabeth went missing and Carter took her place. Which, I have not seen that much of the season yet to be sure how she is but so far its a good decision

[Xaeden]

Political reasons. The IOA agreed to provide the bulk of funding for the Atlantis Expedition on the condition that there was a check on the U.S. military's power. The solution that all parties were able to agree to was the installation of a civilian leader who was respected internationally. The IOA was also hoping that they'd be able to exert a degree of control over her and her decisions, something that would never have been possible with a U.S. military officer in charge. They were unhappy when they learned that Weir had no intention of doing their bidding, but as she noted in "The Intruder" (season 2, episode 2), she had enough support to keep them from ousting her.

The IOA stopped insisting on a civilian leader immediately following what happened to Weir because their fear of a replicator attack outweighed their desire to limit U.S. military control over the expedition. However, as Carter's appointment was based on their fear of an at the moment threat, expect to see more maneuvering for power from the IOA.

[Falcon Horus]

Or... Antarctica does not belong to any one country and most of the members of the expedition are civilians, ranging from most of the countries of the real life Antarctic Treaty.

Also, the Atlantis expedition is/was a civilian expedition with a military contingent, not the other way around.

[Xaeden]

That is essentially why Weir was put in charge of the research team at the Antarctic Outpost:

WEIR: As a matter of fact, the President has asked me to supervise the research of the Ancient outpost. It's gonna be a bit of a delicate situation, given all the various international claims already being made on the site.

-Stargate SG-1, New Order, Part II (Season 8, Episode 2)

However, the decision to allow her to lead the expedition to Pegasus was indeed a politically motivated effort to limit the power and influence of the U.S. military:

WOOLSEY: Look, Pegasus is so far away, they never thought the Wraith would be a threat to anyone outside the members of the expedition itself.

WEIR: It was their objection to having Atlantis under military control that put me in this position in the first place!

WOOLSEY (ruefully): Nothing renews your appreciation for the military like the threat of invasion from life-sucking aliens.

...

WOOLSEY: The I.O.A. has decided that, for the time being, you should continue to head the Atlantis expedition.

WOOLSEY: You're surprised?

WEIR: Yes. I am. I guess this means that international mistrust of the US military is far more powerful than their fear of “life-sucking aliens”.

...

CALDWELL (To Woolsey): That's not why you're here. The I.O.A. doesn't really want militarisation. They're just afraid they may have no other choice.

-Stargate: Atlantis, Misbegotten (Season 3, Episode 2)

It's also worth noting that that the Pentagon believed the international community would have fought against a military leader of SGC had they tried to appoint anyone save O'Neill when Weir left:

WEIR: The Pentagon has convinced the President that there is one man who could run the S.G.C. and make it politically viable from an international perspective, despite the fact that he is part of the American military establishment.

-Stargate SG-1, New Order, Part II (Season 8, Episode 2)

Although there was no mention of what happened to that sentiment when Laundry took over, the balance of power between civilian oversight and the military in charge of the SGC was a continuing plot point after Landry cut a deal to get additional funding from the IOA.

As to what I previously said about the IOA wanting someone they could control as the leader of Atlantis, that was talked about in season 5:

(Cash: I'd avoid reading the following while you're still on season 4 as this quote contains a major season 5 spoiler.)

Spoiler:

TEYLA: I agree. We defeated the Replicators; we thwarted Michael's plans; and the Wraith are in a state of disarray. All of this happened while she was leader of Atlantis.


SHEPPARD: That's the problem.

TEYLA: I don't understand.

SHEPPARD: Well, [Carter's] a victim of her own success. Now that the threat level is down, the I.O.A. is gonna jump at the chance to put a civilian back in command.

McKAY: It's not just that. I mean, Sam didn't exactly stick to protocol.

DEX: Neither did Weir.

McKAY: Right, so for four years they've been waiting to get someone in there who'll finally do things their way.

-Stargate: Atlantis, The Seed (Season 5, Episode 2)

[Cash]

Alright, It explains alot. thank you

[fani]

Weir was quite possibly one of the best commanders of Atlantis. Hammond and Weir were both amazing leaders. Her authoritative voice and good trust of her people was great to watch.
She was truly amazing and I thought it was a terrible decision to let her go. Samantha Carter was absolutely bad at any sort of leadership honestly. She is a terrific scientist/military lady but terrible leader.
O'Neill was great in being decisive and funny while coming across very authoritative. You felt his presence like with Hammond and Weir. Carter was honestly lost in how to command.
And her interaction with McKay was horribly written and McKay was written very badly because no one acts that way and if they did they'd be gone in an instant.
Thankfully the actor redeemed the char in Atlantis and they did a better job with him there to an extent.

I was sad to see Weir go when she was so good and then Carter and Woolsey went from bad to worse.

Shame they had some bad writing for SG1 and Atlantis in S10 and S3-S4. Maybe because of the writers strike but there's no excuse for bad char development and inexplicable action/decision making process.

Still, would have loved more Stargate - another few seasons for all 3 honestly. Shame on SciFi