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The episode starts out with O'Neill's morning arrival. Incidents and minor crises quickly pile up:
The real meat of the story is when SG-1 brings a potential mission to O'Neill. They have learned of a planet formerly possessed by Anubis which Baal has not yet taken over. They have hopes Anubis might have left some useful technology behind, and they even have some kind of remote control device for Anubis's base that was recovered from one of Anubis's Jaffa. O'Neill agrees to the mission, but in an uncharacteristic display of caution, makes SG-1 wait until the following morning to leave, when SG-3 can accompany them as backup. This doesn't make SG-1 happy, because they are impatient (correctly so, since Baal could find the planet at any time), and Carter in particular thinks O'Neill doesn't trust her command skills.
When the mission commences the next day, nothing is found on the planet initially. SG-1 is suddenly beamed away by transport rings (unseen by SG-3). Shortly afterward, an Goa'uld al'kesh ship buzzes the stargate and SG-3. When SG-3 cannot find SG-1, they return to Earth, concluding that a Goa'uld (probably Baal) has captured SG-1.
This hypothesis is apparently confirmed when Baal sends a hologram through the stargate. He offers to trade SG-1 for Camulus, the Goa'uld who requested asylum earlier in the season in "New Order, Part 2". He gives a one day deadline. (Deception #2.)
Camulus is brought to the SGC from where he has been held. He's not very happy with his treatment on Earth, which is essentially that of a prisoner. Consequently, he hasn't been very helpful, and he refuses to divulge any information now. O'Neill takes him to the gate room and orders the stargate dialed up for the exchange with Baal, over the protests of his assistant. He escorts Camulus all the way up to the wormhole's event horizon. Camulus does not cave in. O'Neill gives up on the bluff and returns Camulus to the brig. (Deception #3.)
Upon further reflection, Camulus realizes that Baal will not give up on finding him. However, he doesn't relish being handed over to Baal, so he informs O'Neill of a planet he found with an Ancient device on it. He couldn't figure out how to use it or what it was, but perhaps humans can figure it out. (This should be a warning sign right here - a Goa'uld admitting a weakness?) (Also, deception #4.) If the SGC finds his information useful, they will release him.
When SG-3 visits the planet, they do find an Ancient device, but they also can't figure out what it does. To the more immediate advantage of the SGC, they also find a ZPM (zero point module), which is the power source that is used in Ancient technology, specifically the Ancient base in Antarctica. Since the ZPM has at least partial power, it could be used to power the Ancient defense systems or power the Stargate to call Atlantis in the Pegasus galaxy. However, when Dr. Lee studies the new ZPM more carefully, he realizes that it has been booby-trapped. Some material has been infiltrated into the device so that when it is turned on, a massive explosion will occur. Camulus apparently decided that if he couldn't use the Ancient device, he'd set a trap for whoever did, whether it be Baal or the SGC.
O'Neill arranges a new deal with Camulus: Camulus will take the booby-trapped ZPM to Baal and Baal will return SG-1 (deception #5). Hypothetically, if Camulus gets Baal to use the ZPM, Baal could be destroyed, which is to everyone's advantage. Camulus agrees, and arrangements are made with Baal. But just to show that you can't trust a Goa'uld's word, after Camulus is delivered, Baal fails to return SG-1.
At this point, O'Neill is out of ideas and has used up all his possible advantages. While he's not giving up on SG-1, for the moment he is stymied. But then SG-1 dials back to Earth and requests that the iris be opening quickly, since they are under heavy fire. O'Neill is put into another of Hammond's unenviable situations: if SG-1 had really been in enemy hands, they may be compromised, so they shouldn't be allowed back to Earth. Perhaps O'Neill remembers all the times Hammond bent the rules for him, and allows SG-1 to return home. They reveal that they were never captured by Baal: the rings sent them to Anubis's old base, and they were stuck there trying to figure out how to get out. Baal's forces (on the al'kesh) observed the situation and Baal simply took advantage of it.
The situation seems to have been resolved happily. Carter (upon learning about the booby-trapped ZPM) is regretful that it is now in Baal's hands, where it could be used as a weapon against Earth. O'Neill smugly reveals that he didn't send that ZPM with Camulus - he sent the drained one instead. Just goes to show that O'Neill can play double-cross with the best of them!
The final twist in the episode is when O'Neill's assistant, Gilmor, reveals that he has been on a special assignment by the President to observe and evaluation O'Neill in his new position. O'Neill in turn reveals that he knew about this from the start - General Hammond told him (which he wasn't supposed to).
This episode was done from an unusual perspective: most of the time, we were stuck in the SGC with O'Neill, rather than being a part of the off-world action. O'Neill, like us, rather wistfully watched SG-1 leave through the stargate, obviously wishing he was going with them. We got to see some of the frustration caused by the lack of knowledge of what has happened to SG-1 and the other teams, plus all the small details that are usually in the background. In addition, since O'Neill wasn't able to consult with or confide in his friends on SG-1, we had no idea what he was thinking - for example, the fact that he switched the ZPMs.
The idea of an administrative assistant for O'Neill makes a lot of sense. There are a lot of details and decisions that are not of huge importance, but can only be made at the top, which could be done by an assistant. I actually feel like the assistant's position was similar to that of an executive officer's. For that reason, I was surprised that the assistant was a civilian. Now that Gilmor has left, will O'Neill get a new assistant?
A lot of O'Neill's character came through in true form. He was hugely sarcastic to Baal (even daring to mock him!) and Camulus. He showed that he is not one to stick too closely to the rules, with the diplomats from the other planet or with Camulus. This is especially telling when we find out that he knew all along that Gilmor was evaluating him - and he didn't seem to change a thing. Although, one could say that this is because he was considering resigning (which he mentioned in his letter to Hammond), so he didn't have anything to lose, but I don't think that mattered.
We didn't get to see much of SG-1 in this episode. Carter was reassured that O'Neill has full confidence in her abilities. Teal'c was awfully smily in the bit of time we saw him, when he and Daniel were trying to tempt Carter to get lunch with them.
SG-1's absence (presumably because of capture) showed what lengths O'Neill and the rest of the SGC personnel were willing to go to to get them back. At one point, O'Neill, Major Davis, and Colonel Reynolds (head of SG-3) discuss using the symbiote poison on selected planets controlled by Baal, but O'Neill rejects the idea because of the tremendous Jaffa casualties it would entail, especially since they don't know which planet SG-1 is on. Later, Col. Reynolds and a number of the base personnel put on a quiet demonstration to show that they are ready to support any action by O'Neill to get SG-1 back. This kind of support has to give O'Neill confidence.
I do think that O'Neill made a serious command mistake. Part way through the episode, the super planet has disrupted electronics in the base so that the SGC can not dial out through the stargate. Baal tells them their time is up for agreeing to the prisoner exchange, but O'Neill gets the deadline extended by telling Baal they are having problems and can't dial out. This is revealing a serious weakness to an enemy. Frankly, I'm surprised Baal didn't try to take advantage of it. If the SGC can't dial out, possibly many other systems and defenses were compromised, and an attack by ship might have been successful. Also, we know Baal is an expert in stargate function, so the SGC's loss of function might have provided him with some kind of opening to sabotage their gate system. Fortunately, these things did not happen.
What was the "zero hour" the episode title referred to? I'm not sure. The episode counted down to it, but the zero hour itself corresponded both to the President's arrival at the SGC and O'Neill's decision not to resign. I tend to think the "zero hour" was O'Neill's acceptance of his new position and his realization that he can actually do what is required of him.