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A good part of the early part of the episode is flashbacks, but I'm going to summarize it in straight chronological order. SG-1 makes contact with world they have not explored previously. The world is dominated by two nations, the Rand Protectorate and the Caledonian Federation. The Rand Protectorate has had the stargate in a museum and is surprised when SG-1 uses it.
Over a period of about three months, SG-1 makes numerous trips through the stargate to visit the Rand Protectorate and establish relations. The government is cautiously optimistic about this prospect; the civilization is several decades behind Earth technologically. There are, of course, complications. The Rand Protectorate and the Caledonian Federation have been in a cold war type stalemate for years. While the Rand Protectorate has divulged some information about the stargate and the Earth people, the Caledonians are naturally suspicious. Of even more concern are the religious fanatics who have worshiped the stargate and their ancient "gods" (the Goa'uld, of course) for years; in the past there were few of them, but many people see SG-1's arrival through the stargate as evidence that this religion is correct and so their numbers are growing.
We see a few scenes that indicate that the Rand Protectorate is getting into more and more trouble. The religious zealots have fallen in with a charismatic leader, Soren, who has begun leading them in taking over Protectorate cities and military installations. Caledonia is worried, justifiably so, that if Soren takes over Protectorate military bases that he may use the weapons to attack them. SG-1 tries to help the government of the Protectorate save itself, but it is a losing battle. They feel guilty, especially Daniel, for unintentionally destabilizing this civilization.
Events escalate rapidly. While Carter and Teal'c return to the SGC, Daniel insists on staying on the planet for as long as possible in order to try to stave off war. He stays a little too long. Soren's fanatics take over a key missile base. The Caledonian Federation makes a pre-emptive strike on the Protectorate military installations in order to protect themselves; this attack destroys most of the cities in the Protectorate. Soren's forces attack and take over the military headquarters. Daniel and Jarrod Kane, the second in command of the military, manage to escape, but Daniel is badly injured. The Protectorate's missiles counter-attack Caledonia, but it's not clear whether this was ordered by the government or Soren.
Daniel is nursed back to health by Leda, Kane's wife, at their rural home. Once he is well enough, he tries to contact the SGC with local radio equipment. Meanwhile, O'Neill and SG-1 have been trying to contact Daniel (they don't even know if he's alive). When they contact the planet, they only reach Soren. Soren rebuffs SG-1's visits and attempts to arrange to search for Daniel.
As a last resort, O'Neill invites Soren to visit for negotiations. Soren is a true zealot (and also struck me as a Ben Kingsley wanna-be). O'Neill offers food and medical supplies to help mitigate the disease and starvation that are sure to result from the collapse of the Protectorate infrastructure. Soren rejects this offer and asks for weapons...so he can conquer Caledonia and bring them to the true religion. As one might expect, this attitude doesn't go very far with O'Neill, and Soren is shortly returned to his planet. (Sometimes I think that the SGC is too good - why not keep Soren as a "guest" until things get straightened out?)
Finally Daniel makes contact with the SGC. He arranges a coordinated attack to take out Soren and reclaim the military headquarters, using some SG teams and the remaining forces that Kane has. The attack is successful, and Kane kills Soren. While the country has a lot of rebuilding to do, at least it is no longer under the control of a religious zealot bent on world domination. The SGC promises help in the rebuilding process. The ending is bittersweet, to say the least, given the level of destruction of their society.
This episode had a lot of good issues. As O'Neill says, the SGC is always meddling in other worlds - and sometimes things don't turn out so well. The consequences of contact with the SGC are some of the most severe we have seen - on par with season 4's "The Other Side", which resulted in the annihilation of half of a society, and the continuing problems on Jonas Quinn's homeworld, last seen in season 7's "Fallout". However, as Leda said in this episode, the cold war situation was on a hair trigger and almost any unusual event could have set it off. The religion aspect just set up a third side to the conflict.
We also got to see O'Neill almost lose it, when he snaps at Carter in his office. He had been trying to tolerate Soren's presence and ignorance in the negotiations, and the stress of that, plus Daniel's unknown status, clearly got to him.
Soren was a scary guy. He had quite a presence just by himself, making incredible demands, at the SGC. In the military headquarters, which were about to be overrun, he obviously had his followers captivated. When he commanded them to go out and fight, surely to be killed, and they hesitated, I thought one of them would kill Soren, but no one had the nerve. He believed enough of his own teachings that he was willing to go and fight in person.
Despite the good moral issue of the episode, it lacked something. There wasn't much interaction between the SG-1 members, so we didn't get the usual snappy dialog. The flashbacks to the events before Daniel was injured effectively conveyed the events, but somehow the tension was missing. We also didn't get to really feel the extent of the destruction in the nation because we had almost no look at the annihilated cities or see the attacks - Kane's house was remarkably untouched. While we got to see Daniel smoothly charm another woman, his scenes with Leda were a little slow; I appreciate that it takes a lot of time to recover from injuries, but it seems that many of these scenes were not necessary.
How much help can the SGC and Earth afford to send to all these planets it has promised to help? While I agree that it's the morally correct thing to do, it must be a tremendous drain on resources. We didn't even learn about anything useful the planet might have for us to gain in return.
This episode also made me wonder if the SGC's mission has changed at all. Their previous goal was to find weapons and/or technology to defend themselves against the Goa'uld. Well, now they have them: the Ancient base in Antarctica. Of course, the ZPM that powers it is dead, so finding another one would be good. But otherwise, it seems that the mission could be considered to be fulfilled. I wouldn't be surprised if some opponent of the SGC notices that...