It's a big mystery when it comes to how these three are connected the way they are. You have a device that can destroy or control the Reapers, that not only needs to be attached to the Citadel, but also needs the creator of the Reapers to use it. Lots of speculation. Figured I'd make a thread to help figure things out on what does what, and who was where, and separate a lot of the fiction with facts.
Let's get some things out of the way. I'll be updating all the known facts here, so people can use them to discuss.
1) Where is Shepard when he/she enters the Citadel, and where does he/she make the final choices?
Here, based on the images:


Shepard most likely teleported there (maybe a little closer), because it's the only perspective that allows Shepard to see the bottom arms open, see the Earth from above and the edge of space, and not have the Citadel inner ring get in the way, or the Crucible blocking his/her view.
2) Are the final choices attached or apart of the Crucible or on the Citadel?
Unless everything Shepard saw was all an illusion, the final choices were attached to the Citadel, and not the Crucible. All three choices only effect the energy coming out of the Crucible, into Citadel Tower.

1) Were the choices there before Shepard arrived?
Based on this image, no, unless they were hidden on the surface. Before the Crucible docked, they weren't there at all. They only appeared after. As the Catalyst says, the Crucible changed it. This is one of those changes. Based on the image above, the flat surface split into sections in order to allow the beam from the Crucible to go through.

4) Could the Catalyst make either choice without needing someone?
No. The Catalyst clearly states it can't make them happen, and needs Shepard to act for it.
"The Crucible changed me. Created new possibilities. But I can't make them happen. If there is to be a solution, you must act".
Why, we can only speculate. But if Shepard refuses to use the Crucible, the Catalyst doesn't use it, and instead shuts it off. Proof that for whatever the reason, it needs Shepard to make the choice, or it is never done.
5) Was the Crucible originally made to work with the Citadel and/or the Reaper AI?
From what Vendetta (the Prothean VI) claims, it was not.
"The plans for the crucible were pasted down to us from the previous cycle. And countless cycles before that. At some point, it is difficult to pin point when, the crucible where adapted to incorporate the use of the Catalyst. Presumably, the crucible was not sufficiently powerful enough to defeat the Reapers."
6) What does the Citadel or Reaper AI do with the Crucible?
Vendetta makes the following claim:
"The Catalyst enhances Dark Energy transmissions, and coordinates the entire Mass Relay Network."
The Catalyst claims:
"The Device you refer to as the crucible is little more then a power source. However, in combination with the Citadel and the mass relays, it is capable of releasing tremendous amounts of energy throughout the galaxy. It is crude but effective and adaptive in its design.
7) Who designed the Crucible?
The Catalysts claims we don't know them, and there's not enough time to explain.
However, this does not answer who "adapted" the plans to the citadel.





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