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SG-1 returns from exploring a new planet. Like usual, they are greeted by General Hammond and sent to the infirmary for the standard medical check-up. Instead of receiving their routine shot, they are drugged and knocked out.
Teal'c wakes up on a stretcher and overhears Dr. Fraiser and General Hammond discussing their takeover of the SGC; he also sees two alien beings involved in the discussion. Teal'c concludes that the aliens have some how replaced or duplicated Fraiser and Hammond (and possibly others), and he's in imminent danger. He fakes unconsciousness until he has the opportunity to disable his guards.
Teal'c finds the still-unconscious Carter and revives her, since he had heard the aliens discussing how he and Carter were resisting whatever treatment was being given them. Carter and Teal'c realize that they have no idea which SGC personnel have been taken over and/or replaced, and so they plan to escape the SGC and bring in reinforcements to re-take the SGC.
However, the aliens discover that Teal'c and Carter are missing and raise the alert. Teal'c distracts the aliens while Carter escapes. Teal'c does a respectable job of taking out alien guards before he is recaptured.
Carter isn't sure how far up the chain of command the aliens have infiltrated, so she crosses chains of command and contacts Col. Harry Maybourne, whom we last encountered in season 2 in "Touchstone". Even though Maybourne isn't in the SGC's chain of command, he's clearly aware of the "foothold" situation Carter states. He agrees to meet Carter in Washington, DC.
Carter's meeting with Maybourne quickly turns sour, when O'Neill and Daniel show up. Maybourne said the SGC called him, and he spilled the beans. The SGC's story is that there was a chemical spill (that was, in fact, mentioned when SG-1 returned through the Stargate), and Carter is having paranoid hallucinations because of chemical poisoning. Carter is livid that Maybourne went against protocol and communicated with the SGC, but O'Neill and Daniel are oh-so-convincing. They soothe Carter and eventually talk her into returning to the SGC, along with Maybourne, to show her that there is no alien infiltration and treat her chemical poisoning.
Back in the SGC, the supposed Dr. Fraiser and Hammond are feeding Teal'c a similar line about chemical effects, trying to get him to tell them where Carter went. As soon as they hear that Carter is flying back to the SGC, they drop the pretense and start discussing the experiments they will conduct on Teal'c - chilling!
On the plane (which is very luxurious), Carter is still paranoid about being near O'Neill and Daniel, but Maybourne doesn't take the situation seriously. Suddenly, something happens, and O'Neill's image flutters between that of O'Neill and an alien. Carter grabs Maybourne's gun and shoots O'Neill. He apparently dies. Major Davis, who was liaising with them for the SGC, roars into action to attack Carter, but she shoots him, too.
Maybourne is now convinced that the aliens have in fact infiltrated the SGC. He tries to interrogate the alien Daniel, who doesn't cooperate and ends up being shot, too, but only injured.
When Carter investigates O'Neill's corpse and the alien posing as Daniel, she finds two alien devices on them. When the first one is removed from the corpse, the image of O'Neill disappears and the alien's true appearance is revealed. The device apparently creates an essentially perfect illusion of being another person. Carter takes Daniel's illusion-making device is able to use it on herself. The second device's use is more ambiguous, but Carter guesses that it somehow creates a mental conduit between the alien and the human, so that the alien can act like the human and access his memories.
Carter and Maybourne devise a plan: Carter will return to the SGC and try to regain control of it with Teal'c. If she isn't successful within a certain period of time, Maybourne will attack with other military personnel.
Meanwhile, at the SGC, the real O'Neill and Davis awaken in a room filled with other unconscious personnel. All of them are suspended in some kind of alien harnesses. The harnesses apparently keep them bound and hooked into the mental system the aliens use to impersonate them. We, the viewers, realize that O'Neill and Davis became conscious when their alien counterparts were killed. O'Neill and Davis manage to escape from their harnesses just in time for Carter, disguised as Daniel, to find them.
O'Neill and Davis connect up with Teal'c to start re-taking the base. Carter goes to her lab to try to reproduce the conditions that caused the alien illusion device to malfunction - it was caused by just the right buzzing tone. She transmits the tone throughout the SGC, and the aliens are all revealed. They realize that their plan has failed and begin evacuating through the Stargate.
Carter and O'Neill manage to get to the control room and close the wormhole as Maybourne and his forces storm the base. The aliens that are trapped in the SGC self-destruct, damaging the control room and effectively preventing any interrogation or intelligence-gathering about them.
This episode was fun, albeit having a few plot holes. Certainly alien infiltration would be a concern of the SGC's and the government's, so it's good to see that there are plans in place to deal with the possibility.
One of the biggest plot holes is the speed with which the aliens apparently took over the SGC. From what we could tell, SG-1 had only been absent a few hours on their planetary reconnaissance (because they didn't find anything except "rain"), and the aliens managed to replace everyone during that time. If you know what you're watching for, though, there is some nice writing when SG-1 returns. Notice that upon their return, General Hammond doesn't say much of anything - O'Neill does all the talking. Similarly, Dr. Fraiser sticks strictly to by-the-book interaction, presumably so the alien mimicking her doesn't screw anything up.
The second big plot hole is that the aliens had a bunch of the harness-devices perfectly sized and attuned to humans that they could use so quickly. The shapes and sizes of the harnesses seemed pretty customized. Had the aliens somehow been planning this infiltration for awhile? Did they get prior information of humans and/or Earth?
Specificity to humans aside, the alien devices were clever, in that they provided a means for the aliens to successfully replace specific humans: the mental link gave them the memories and behaviors they could employ. This is something that alien-invasion plots often overlook - aliens are very unlikely to be able to mimic specific humans very well. The personal-illusion-generator was also very clever.
I did like that the episode did not try to keep the alien infiltration a mystery from the viewers for too long - the inconsistencies would have added up too much. Instead, I appreciated that the plot was about how to re-take the SGC. It did make sense that Carter and Teal'c were the two "odd" beings in the SGC that might cause problems.
Maybourne was a good addition to this episode. He's a character that we, the viewers, know well, and Carter was correct that he was pretty dissociated from the SGC and not someone she was likely to contact except in emergency. Despite not taking the situation seriously at first, he proved to be an effective ally in the end. The creator of Babylon 5, JMS, said that the "bad guy" character in a series can't always be wrong and/or incompetent, because then the character loses credibility. Here, Maybourne does get the chance to be on the "right" side.
How will this episode affect the series? Well, given the ease with which the SGC was taken over, they seriously need to reconsider some of their protocols and security. I don't think Hammond's comment at the end that all they could do was change all their codes was really a good response. They will also blast the buzzing tone at all returning teams. How long until the aliens change their technology to fix that problem? They have locked out the planet that the aliens evacuated to - will they ever investigate it?
The SGC (or maybe Maybourne's people) now has access to the person-illusion-generators that they got from a few of the aliens. They should have the ones that generate illusions of Daniel, O'Neill, Davis, and Fraiser, at least. Will they be able to figure out the technology and make ones for other people? Or simply just "cloaking devices" for people? Something like this could be a huge tactical advantage, both in battle and in covert operations.