So I decided to think of a way how the Catalyst can exist alongside the events of ME1 without being a plot hole
This is going to contain a heavy dose of headcanon.
The Citadel is part of me
First, I want to address Catalyst's words in ME3.
Now, if we take these words literally it'll throw a wrench into the whole ending of ME1 when
1) A vanguard Reaper was left to send a signal to the keepers - the Catalyst could've done so itself
2) Prothean scientists were able to alter the signal without the Catalyst noticing
3) Vigil data file allowed to override station's security systems.
4) Sovereign needed to override station's security systems to open the relay
All of this boils to Prothean scientists making modifications to the Citadel which is "part of me" as the Catalyst says it (if we take it literally).
I think that "the Catalyst" acts as a homonym in this case. The child says:
Consider for a moment, that Shepard refers to the Catalyst as the missing component of the Crucible while the child refers to the aforementioned catalyst for peace. If that's the case, the phrase "The Citadel is part of me" means "The Citadel is part of the catalyst for peace between organics and synthetics" which works since the Citadel is an integral part of the child's 'solution'.
Reaper independence
The second point I want to address is the child controlling the Reapers. It says:
Now, if we consider the Reapers as simple pawns moved by a mastermind in form of the child, it contradicts their independent actions and personalities.
I think that the Reapers act independently. The child says
What I think this means is that 1) the Reapers are created in the form of Leviathans 2) their task is the preservation of organics and synthetics 3) the data they collect is then used by the child in search of a new solution.
The Reapers continue the process started by the pawns. I think the Reapers are autonomous in their search and acquisition of data and the Catalyst can assume control at any moment. I think that in Control ending, Shepard assumes control and changes their function. Preserve becomes protect.
The Catalyst's actual power over the Citadel
In Control ending we see the Citadel arms closing which means that the Catalyst can control them. But that would mean that Vigil's data file overrides Catalyst's systems? Or that Sovereign needs to do the same, despite being the Catalyst's creation?
Personally, I think that the Catalyst is in hibernation until the genetic material is brought to the Citadel to create a new Reaper. It coincides well with the previous supposition of independent state of the Reapers. The Catalyst's function is not to oversee the harvest, it's finding a solution based on the physical data collected by the Reapers. There is no reason for it to be active before having access to the data. That means it is only 'wakes up' after the Citadel is moved to Earth.
The Collectors were simply laying groundwork for the human Reaper.
"They are going to target Earth"
We all know they would not have been able to do it with their one ship. My guess is that the Collector Base was creating the Reaper core and would've moved it to the Citadel once it was completed. Then they would've connected it (giving the Catalyst access to its data) and finalized the construction on the Citadel by building the cuttlefish shell over it.
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