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At the beginning of the episode, SG-1 arrives on a new planet, entering an underground facility. They begin exploring. Daniel and Carter find an interesting collection of artifacts that the natives apparently gathered while exploring other worlds. Meanwhile, O'Neill and Teal'c come upon an unusual metal emblem. Teal'c says it's a warning posted by the Goa'uld for other Goa'uld: the world's surface has been destroyed by the Goa'uld, and the planet is unsafe. Teal'c convinces O'Neill that they should leave immediately.
O'Neill orders them to prepare to leave. Daniel is frustrated by having to leave all the artifacts behind and lingers to scoop bunch of them into his backpack. When he handles one device, an object that appears to be a mirror turns on. Daniel examines the mirror, but oddly, while it shows a reflection of the room he's in, it doesn't show him. He touches the mirror's surface, and we see him enveloped by energy. Excited by the discovery of this device, Daniel runs to get the others to help him take it back to the Earth. However, everyone else is gone. Daniel thinks they've pulled a practical joke on him and dials the Stargate back to the Earth.
When he arrives at the SGC, he finds a bunch of troopers with guns trained on him. He's confronted by Colonel Hammond, who demands to know how Daniel got an identification signal device to return to the Earth. Daniel is flabbergasted. In short order, despite his protests that he's a member of SG-1, he's sedated and given an MRI to ensure he is not possessed by a Goa'uld.
When he wakes up, he's locked in a cell. Catherine Langford (the original scientist studying the Stargate, whom we met in "The Torment of Tantalus") comes to question him about how he came through the Stargate. Daniel is still so confused about why no one knows him and why things are the same, yet different. He (and we) gradually learn more. Catherine is still the head scientist working on the Stargate; Daniel had turned down Catherine's offer (in the original Stargate movie) to study the Stargate. Carter is not in the military, but is a research scientist under Catherine. O'Neill is the general in charge of the SGC.
Daniel knows enough about Catherine, the others, and the Stargate program for Catherine to be curious about where he's from and to think that he might have information that is helpful to them. She takes him to talk to O'Neill, who is short on patience (the same as in our universe!). When Daniel reveals that Teal'c, Apophis's First Prime, is actually their ally, O'Neill is ready to dismiss Daniel. Catherine convinces him that Daniel could still be useful. During the discussion, Daniel mentions that he knows the Stargate address for Chulak, and O'Neill is happy to gain this key piece of information.
Catherine and Carter reveal to Daniel that the Earth is currently undergoing an invasion by the Goa'uld. A lot of the east cost of the US and other large cities world-wide have been destroyed. The Goa'uld are systematically destroying lesser targets, razing the surface. We learn that O'Neill went on a mission to Abydos to destroy the Stargate there with a nuke, like in the original Stargate movie. We're not sure exactly how events unfolded there, but they proceeded without Daniel's influence, and now Apophis has tracked that attack back to the Earth.
In short order, events escalate. The Goa'uld have been dialing the Earth's Stargate and keeping the wormhole open in order to prevent the Earth from using it. However, they can only keep it open for 38 minutes. At the next break, O'Neill sends a nuke through the Stargate to Chulak over Daniel's protests. The SGC has been evacuating key people to another planet to try to continue the human race. The President of the US is on the way on Air Force One, but is killed by the Goa'uld. Apophis's huge pyramid ship lands on top of Cheyenne Mountain, above the SGC.
During all this, Daniel is still trying to figure out what has happened to him. He speculates that he's in another dimension. Carter jumps on this scientific idea with her usual enthusiasm, saying it's possible that he's in an alternate universe. Carter, Catherine, and he realized that the mirror artifact that he touched on the other planet must have somehow moved him from one universe to another.
The Goa'uld are quickly breaking through the SGC's defenses. O'Neill intends to evacuate as many people as possible to the alternate planet when they get the next break in the Goa'uld tying up the Stargate. Daniel beseeches him instead to send him back to the planet with the mirror so that he can return to his own universe, warn them about this imminent Goa'uld attack, and at least save the Earth in an alternate universe. Implicit in his request is the idea that the Earth in this universe is lost.
They need more time until the Goa'uld will have to stop the wormhole. Daniel convinces O'Neill to talk to Teal'c and try to convince him to turn against Apophis. He produces his videotape from the beginning of the episode (taken in the real universe), which shows Teal'c working with SG-1. For some reason, O'Neill agrees.
We've seen Teal'c stomping around and personally leading the attack on the SGC. O'Neill surrenders to him and somehow convinces him to watch Daniel's videotape. Teal'c is clearly puzzled by O'Neill's story and the video, as well as the fact that O'Neill knows Rya'c's name (from Daniel), but he's too pissed off at the nuke that destroyed Chulak and his family to be agreeable. He kills O'Neill.
Near the Stargate, Colonel Hammond lines everyone except for Carter, Catherine, and Daniel up for a last stand against the Goa'uld. The base self-destruct has been set for 2 minutes after the Goa'uld should have to stop connecting to the Stargate again. Hammond fights until he's out of bullets and is shot.
Carter is trapped by Jaffa in the conference room above the gateroom. She takes them out as well as herself with a couple hand grenades. The Goa'uld wormhole closes and the Stargate dials the planet with the mirror. As Daniel waits in the gateroom, Catherine is taken by Jaffa. The Jaffa blast into the gateroom, and Teal'c enters as the Stargate's wormhole forms. Daniel runs through the Stargate, with Teal'c shooting him in the back. The self-destruct counts down (in a scene that reminds me of the Klingons on the self-destructing Enterprise in Star Trek III: The Search for Spock) and destroys the Stargate, Teal'c, and Cheyenne Mountain.
Daniel arrives on the mirror planet and manages to make his way to and through the mirror, despite his injury. In our universe, the rest of SG-1 is still searching for him and hear him collapse as he returns. As the episode closes, Daniel warns O'Neill that the Goa'uld are coming and releases the piece of paper with the Stargate coordinates of the origin of the Goa'uld attack.
This was quite a thrilling episode. It's very affecting to see all the characters we know and love die, along with the Earth, even if they aren't in "our" universe. The main reason I don't give this episode the highest rating is because the events in it aren't "real" in the sense of happening within our universe, so it's bit of wish-fulfillment in terms of seeing what would happen if everything went wrong. I also really enjoyed how the events in this episode explicitly connected back to previous Stargate SG-1 episodes and the Stargate movie.
The Many Worlds Theory that Carter describes is a legitimate speculation in physics. The idea is that for every action you take, such as deciding to go to the movies or stay home and watch TV, two universe are generated: one in which you go to the movies, and one in which you stay home. Each universe then proceeds to evolve from that choice. For each additional choice that each person makes, more and more universes are generated. Obviously this would generate an uncountable number of universes as billions of people in each universe make choices. Some universes would be very similar to each other, since the choices (such as go to the movies or stay home) don't change the people or their surroundings much. Other choices have more influence - for example, imagine the choice of using the atomic bomb at Hiroshima or not. Those choices cause major differences between the universes. However, the Many Worlds Theory is more accurately called a hypothesis, because it has not been tested in any way. It's great fodder for science fiction, though.
What choices have been made that make this alternate universe so different from our own? One of the major choices seems to have been Daniel's decision in the alternate universe to not join the Stargate program. I can see how this would have major effects. In the Stargate movie, Daniel moderated and influenced O'Neill's interactions with the people on Abydos. In addition, he stayed behind on Abydos and married Sha're. Then in "Children of the Gods", O'Neill had someone to contact on Abydos for information about the Goa'uld. The knowledge Daniel gained on Abydos enabled the SGC to more effectively use the Stargate. In addition, Daniel's inclusion on the mission to Chulak in order to search for Sha're may have influenced O'Neill and Teal'c's actions.
The consequences of choices the characters make is seen throughout this episode. A lot of O'Neill's choices come back to bit him here. He chose to use the nuke on Abydos as ordered originally in the Stargate movie, which seems to have been the impetus for Apophis's attack. In this episode, he sends a nuclear bomb to Chulak, which rebounds on him in short order as Teal'c cites it as a reason to take revenge on O'Neill. Daniel had chosen not to join the Stargate program and was killed in Egypt by the Goa'uld invasion. (I loved his comment upon realizing his alternate-universe self was dead: "Oops. I think I'm dead.")
Carter had chosen not to join the Air Force. This is a bit of a superfluous change, as she still is integral to the science program involving the Stargate. It's also not very enlightening, as we didn't know why she chose to join the Air Force in our universe, and we don't know why she didn't in this universe. However, it does give the writers the opportunity to make her and O'Neill a couple. It was amusing how they rigidly followed protocol and gave no clue about their relationship until O'Neill was about to go off and die.
Conversely, the Teal'c of this universe did not have as many choices to make. He never encountered O'Neill and Daniel on Chulak and given the opportunity to choose to betray Apophis. At the time of the events of this episode, that choice was moot, since Chulak, his family, and many of the Jaffa that he wanted to free were dead.
Honestly, I'm not sure why General O'Neill decided to grant Daniel's request to be returned to the mirror planet so he could save the alternate Earth. O'Neill probably should've used the last Stargate access to send a few more people through to the alternate planet. Although as it turned out, there would've been very little time for any additional people to go. I feel like O'Neill's agreement to Daniel's plan was an admission that this universe's Earth was lost, and so he would at least have the possibility of saving an alternate Earth.
While I said that the events of this episode don't really matter, there is one effect in our universe: Daniel may have warned the SGC of an upcoming Goa'uld attack. However, because of the differences between the universe, it does not seem like such an attack is guaranteed, nor would it necessarily be originating from the same Goa'uld planet. After all, in our universe, there are significant differences in how the Goa'uld have been affected by the SGC: Ra was killed; Apophis lost his First Prime; Hathor was awoken and left the Earth to go to Chulak; SG-1's visit to the Nox's planet had Apophis removed from that planet. While I think that Apophis is probably ticked off at the Earth, some of these events might get him to plan an attack differently. Even so, Daniel's information about the attack should certainly be investigated.
The other effect this episode will have on the real universe is that now the SGC has the mirror artifact that transported Daniel to the alternate universe, which future episodes will call the quantum mirror. At this point, it's not clear what they will be able to do with it, because the alternate universe Carter blew up the control device along with herself and the Jaffa. If they can't change the mirror to another universe to visit, it won't be very useful, as the Earth in that universe is destroyed.