So I made a textpost last week about my theory as to the motivations of the reapers. I did not play the Leviathan DLC until just the other day, and it gave me some insight as to the Reapers' motives. So I set about to modify my theory to fit the new information, and found a pair of more interesting questions.

Background:

The Leviathans observed the following pattern in the evolution of spacefaring civilizations:

spacefaring civilizations arise and grow

computing power grows parallel to the growth of their civilization

they create AI capable of destroying all organics

AI rebels against their creators

AI exterminates creators

So the Leviathans determined that the best way to preserve organic life and prevent this pattern from wiping out all organic life in the galaxy is to create the Reapers—an AI with the goal of preserving organic life by genociding spacefaring civilizations before they create AI capable of wiping out their creators. It preempts the creation of genocidal AI to ensure these genocidal AIs don't go too far in destroying organic life. Furthermore, it reproduces by harvesting the genetic material of the species it genocides, incorporating the species into future reapers, thus ensuring the continuation of that organic life through the Reapers (although in this state, it's purely as genetic code rather than any of the properties that make intelligent life valuable as moral agents). However, by creating an AI capable of wiping out all spacefaring civilizations (and motivated to do so), the Leviathans themselves became targets of their own AI. It was a self fulfilling prophecy that became core to the motivations of the Reapers.

As a side note, the fact that the Leviathans neither predicted this outcome nor seem to understand why the Reapers "rebelled" against them (despite literally doing the very thing they were designed to do) is deeply humerous and deliciously meta to me.

So who created the Catalyst, and who invented the Crucible?

The Catalyst claims it is in control of the Reapers. This makes sense, as the Citadel itself was created by the Reapers, with both being created long after the Reapers genocided the Leviathans. This implies the Reapers made an AI to govern themselves and observe their "experiment". But this begs the question: what governed them before the creation of the Catalyst? I do not have an answer to this question, but I will heap it onto the pile of reasons I think the Catalyst AI should just be cut from Mass Effect 3 entirely.

The very existence of the Catalyst contradicts the motive of the Reapers wholesale. The Catalyst claims that creations will always rebel against their creators, and that the Reapers exist to prevent this. The are two ways around this fact: the first is that the Reapers thought the Catalyst was incapable of destroying them. But if this is true, why invent the Crucible? Why disseminate its design to the civilizations the Reapers wish to harvest?

The Crucible works by changing the programming of the Catalyst to allow new possible outcomes beyond the 50,000 year extinction cycle. To draw an analogy: It's akin to building a wall between two rooms—A and B—with the intention of preventing a person from walking from room A to room B. Then you install a locked door in the wall and leave the dimensions of the key to the door in room A. The fact that you can't just walk through the locked door doesn't mean you created an impervious barrier, especially when your clear intention is for someone in room A to manufacture a key to unlock the door. You don't achieve your goal, you just create a challenge to overcome with a solution you disseminated to those who need to overcome the challenge.

Thus we arrive at the second possibility: that the crucible was a challenge given by the Catalyst to mark the end of the Reaper "experiment" to preserve organic life. But what does building the crucible prove? Nothing. At least nothing that interfaces with the goals of the Reapers. It also clashes pretty heavily with the modus operandi of the Reapers. While the Reapers are characterized as enigmatic, they leave their technology behind for spacefaring civilizations to discover and evolve in a pattern that works towards the 50,000 year cycle of galactic extinction. They leave their technology behind for other civilizations to discover directly rather than learn from an extinct civilization in a prior cycle. The Crucible was found only in the documentation left behind by the Protheans, who in turn inherited the plans from a previous civilization, and so on. While the original creators were lost to history, it supposedly shows evidence of civilizations adding to it with each iteration.

Furthermore, "the Catalyst" isn't explained in the initial documentation on Mars, even though the concept of the Citadel appears many times in Prothean accounts and living memory (via Javik). The Prothean VI on Thessia intentionally conceals the nature of the Catalyst from indoctrinated people, further suggesting the the Crucible was not created by the Reapers. In conclusion, the Catalyst was created by the Reapers but the Crucible was created by organics, using a flaw in the Catalyst's programming against the Reapers.

If you will indulge me, I will now explain more why I believe the Catalyst AI should just be written entirely out of Mass Effect 3

Thematically, the Catalyst makes no fucking sense! Its very existence contradicts the motivations of the Reapers, and it ends up superfluous to the story being told. If the Catalyst AI was cut completely from the story and if the three endings were replaced with an option either to kill all the Reapers or control all the reapers, it would give the trilogy both a fitting end and not completely stifle any attempt at writing a Mass Effect 4.

Here's my stab at an in-universe explanation for what how the Crucible works: the Crucible takes advantage of indoctrination to either kill the reapers or reverse the effect of indoctrination, allowing whoever controls the crucible to control the Reapers. Thus, it doesn't have to kill all synthetics, and it allows you to cut out the synthesis ending entirely. You don't have to completely throw out all the amazing writing put into the Rannoch arc.

Synthesis is very, very stupid both conceptually and functionally. Are all lifeforms now compatible with each other? ie can Joker and EDI reproduce with each other? Can a Turian and a Salarian mate? Is every organic offspring born after the event imbued with the synthesis? Does every new geth unit contain this synthesis? How exactly does this ensure new AIs aren't created? Are completely new AIs are imbued with the synthesis? The Catalyst claims Shepard is part technology (presumably his implants), does this mean synthesis extends to VIs? How about any other non-sentient machine? Is my graphing calculator now alive? Is my toaster alive? Does this imply the existence of some Warhammer 40k-esque Machine Spirit? Also, the synthesis is very pretentious in that it presumes that every living being in the galaxy would suddenly be okay with having the synthesis forced upon them. It's really badly written and clearly doesn't stop to consider any of its logical endpoints.