Didn't Daniels say that it wasn't supposed to happen, when this whole thing got underway too? Of course this whole thing is going to be a reset switch type situation, it can't be anything else, imo. If you ask me though, the whole setup for the episode was rediculous. It takes time for a change in the past to ripple up to the later time and register? How much time, and why? What's the deal with that, and since they are time traveling, don't they have all the time in the world to setup a party to go back and nuke the problem? What's with the "it took so much time to get approval just for me to make contact with you, but there isn't time for...." I even if time was a factor (which it shouldn't be, since they are dealing with going back and fixing a problem that apparently didn't wipe them out entirely) wouldn't it take more time to get approval to use their equipment to send Archer and another person (a person who was relatively uncontaminated by the idea of time travel 'til now, mind you) than it would for Daniels and a couple of other agents to go back and fix the problem themselves? Just doesn't wash, if you ask me (the episode was pretty good, except for a few of those things, but since the core was bad...
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Their time travel writing is lazy/sloppy to the extreme, and they need to just let it die out after they finish the Xindi thing, and move back to something simpler, like the Vulcan/Andorian thing, but they clearly MUST do these things, especially since they don't have a holodeck to do their little throw away stories with because they don't have what it takes to build a larger scale story that doesn't need over half a season of filler or episodes which only partially pertain to the overall storyline. Oh, well.