The answer? The Catalyst does not actually exist.
Let's look at the Crucible: which civilization was the last to build and improve its design? The Protheans. Javik specifically said that their technology communicate through neural interface. The Beacons transmit thoughts and ideas directly into its users instead of telling them the message via words and sound. Therefore, I posit that the Protheans integrated this technology into the Crucible as part of its control interface.
What was the last thing we see before Shepard meets the Catalyst? Shepard collapses and a bright flash engulfs the screen. When this happens, Shepard's mind is directly linked to the Crucible control and everything we see is happening in Shepard's head. Immediately after the flash the Citadel arms open fully. The moment Shepard interfaced with the Crucible, the activation sequence had begun.
Each option we see is the symbolic representation of its consequence. In Destroy, Shepard uses a weapon to literally destroy a power conduit. In Control, Shepard takes hold of two control pillars. In Synthesis, Shepard embraces the Crucible beam and becomes one with everything.
So what is the Catalyst then, if it doesn't actually exist? The Catalyst is actually Shepard's doubts and fears. From the start of his journey, the child has been haunting Shepard, that humanity may not survive the war, that he might fail in his mission. We see this in Shepard's recurring nightmares.
The child is a way for Shepard's mind to make sense of the ordeal. He is essentially dreaming up the Catalyst to explain away why things are the way they are. Shepard doesn't question its logic because nobody thinks dreams are weird when they are dreaming. If Shepard has a low EMS, the Catalyst asks "why are you here", as if his doubts and fears know that Shepard hasn't done everything possible to bring the galaxy together.
"Wait, but how does this fit into the Control ending", you ask? "Doesn't Shepard replace the Catalyst"?
No he doesn't. You cannot replace something that never existed. When Shepard chooses Control, his consciousness (still linked to Crucible) is embedded in a data burst and sent out across the galaxy to overwrite the core programming of every Reaper. Once taken Control, Shepard's mind literally exists in every Reaper. He becomes the "collective intelligence of the Reapers". This explains why you need to fire the Crucible in the Control choice. After all, if you are just taking over control from the Catalyst, you can just send out instructions the same way the Catalyst did, without the need of a giant blue bubble.
My hypothesis eliminates the inconsistency between previous games and this one since nothing is really controlling the Reapers and the Catalyst really is just the Citadel, and not a translucent kid living there. All insanities spouted by the Catalyst are just the inner conflicts of an unconscious mind exhausted from war and injury.
Furthermore, there is no secret room on the bottom of the Citadel tower with three retractable catwalks just waiting for someone to dock a Crucible. The collective efforts of the Cycles before us did not forget to include an activation switch and instead relied on its user shooting up the place. The hypothesis is not as extreme as to disclaim the existence of everything (ie. IT), but not as naive as to take everything at its face value.
It is, dare I say, the perfect solution...





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