I honestly really liked where you had the idea end! The adventure of figuring out the anomaly and making sense of the property and everything just for them to return to the cell and it is gone is a fantastic end to the article in my opinion!
Hmm. I agree that it's a good ending for the sake of a story, but then with regard to the SCP article, what do I say about it's existence? Is it completely gone from our dimension now? If so, no containment protocol is required, negating the need for an article… right? Or am I misunderstanding something? I had intended universe Z as the reason for the flower to go missing from our containment cell, just as we "stole" it from universe X's containment cell. The slightly off-synch (by minutes, probably) time difference between the universes was the cause of the issue more so than the movement itself. Or, that was what I initially intended.
How did you originally interpret the missing flower at the end of the story? Why do you think it went missing? And, based on what you inferred from the narrative, do you think our version of the flower shop still serves as a gateway to the dimension, even though (scraping the recursive bits) we did not interact with personnel from a universe Z? I'm trying to understand how the story still makes sense without that content. I'm sure we're interpreting it differently, which is perfectly fine. Yours sounds like it may be cleaner, actually.
What is listed after that point doesn't seem to hit a second apex or critical idea so the idea feels like it blows past the satisfying ending and the rest just drags. I would recommend thinking about this second half and what it is adding to the narrative and what new things it is giving to the reader to keep them interested.
My thought was that the last portion would drive home the bootstrap recursion concept. A reader might think, "Wait a minute. So if universe Z stole the flower from universe Y, and universe Y stole the flower from universe X, then where did this cycle start? Is there a start? Is there an end? Universe Y knew how to interact with and instruct universe Z based on being instructed themselves by universe X, who knew how to instruct universe Y through being instructed by universe W." It's meant to be a chain reaction that has no beginning or end. This may be too convoluted, and I don't really have a problem scrapping the bootstrap recursion stuff altogether. But, if I do scrap it, I'm not sure how I would interpret the ending. It seems like there'd need to be a follow-up of our Foundation verifying the dimension's existence and accessibility through the flower shop, and deciding to ignore who stole the flower by simply building a Site around the shop. If the shop is no longer a gateway to the dimension, I don't see the need for a containment protocol.
If I may, and please take this as brainstorming and not as me overruling your idea or trying to interfere with your process, but what if the butterflies come from people and other creatures being in the room when the flower is moved? If a person from universe X is in the pocket dimension with the flower and someone from Universe Y takes the flower out of the pocket dimension then all doors slam shut after the flower crosses the threshold (even with observation) and they become one or more butterflies in the next location's pocket dimension. Something like this could tie up your loose connections between the flower wanting to be moved, butterflies coming from animals and people, and the butterfly creation effect with the localized pocket dimension effect.
Pedagon: *mic drops* (lol)
That's cool. If this is how it works, it almost seems like… when you pick up the flower, the door has to reappear. And maybe the only way to get the door to reappear is by holding the flower. It won't let you leave the dimension without it. In this case… so, it's already established that universe X and Y are accessing the same pocket dimension (not just their version of it), and that's a core piece of the narrative that leads to the ending you like. This implies that in order for anyone to ever turn into a butterfly, groups of individuals have to go into the dimension together, and one ***hole has to leave with the flower, abandoning their peers and condemning them unwillingly or not. You'd think that once someone held the flower and saw the door reappear, they'd let their peers know about it and try to get them to come with. I guess if they did leave, the door would still shut behind whoever was in line behind the person holding the flower. In any case, it seems strange for there to be billions or trillions of butterflies.
One option: it could be that the dimension collects a large number of individuals before the flower's hypnotic properties "activate," or something, and the Foundation happened to come across it at a time when it was very recently moved (because there were no humans inside at that time).
Another option: it could be that the door opens into a random location within the dimension, rather than right next to the flower. This opens up way more narrative possibilities regarding exploration logs. Depending on how long this anomalous flower has existed, you could come across ruins of a civilization being taken over by nature, since that civilization was turned into butterflies long ago. It almost makes more sense that you would encounter wandering humans in this dimension if (1) the door leads to a random location within it, and (2) the only way to leave is to find the flower and leave your people behind. THAT idea seems more reasonable, in that the flower has only been moved a handful of times (i.e. not constantly). Holy cow, you could have… perhaps the owner of the shop was born in this dimension, and growing flowers is all he knows how to do. He finds the flower, leaves the dimension, adjusts to society based on stories from his great grandparents, starts his own flower shop, enters the dimension by accident, attempts to rescue his family, and, well… that's one tragic oopsy-daisy. He exits the dimension, kills himself, the shop is purchased by the bank, the bank sells it to someone, etc., that shop goes on.
Sorry, I just ran with it :). Any thoughts? I'm totally down for brainstorming if you want to PM me.