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As for why he didn't just roll in and activate the citadel manually himself, I'm not entirely sure if that's ever addressed. You could chalk it up to him being unable to return to citadel space without also being under a very watchful eye, because of accusations and evidence against him.
Such as how you can recieve a microphone from the reporter to bug the ATC for a quest on the citadel... but if you dont do it then canonically Shepard has a recording device on him when talking to Sovereign but doesnt use it because :P
The primary mission of Sovereign and therefore Saren is activating the relay, before Eden Prime Saren was completely trusted and respected so he could have gone directly to the citadel activate it without any issue whatsoever, Sovereign would never have delayed this so Saren could go check out a protean device and risk everything for simple curiosity.
Also if Saren could understand the beacon thanks to Sovereign and this makes perfect sense by the way, Sovereign would have indoctrinated a fair number of Proteans in the previous cycle and if he can talk with us in this one he could in the previous so he knows the language.
But then what's the point of going to the thorian get a cipher to be able to understand the beacon ? For us sure but not for Saren and if he hadn't gone there we would never have known at all. Doesn't make any sense at all.
Reapers are tough, but they aren't invincible. Outright attacking something as heavily defended as the Citadel is a bad strategic move without some kind of failsafe. Sovereign loses his failsafe when Shepherd follows Saren through the Conduit, something the heretics failed to prevent from Eden Prime to Ilos. As for the language thing and needing the Thorian, I can see that being a problem I suppose. At the very least it means Sovereigns window into Sarens mind was still limited, but he knew enough to know the conduit exists. I'm just saying, the protheans weren't exactly easy for the reapers to exterminate. It took CENTURIES because the protheans were quite advanced and had a vast empire. They scorched entire worlds to slow the reapers down, they fought the kind of war you fight for survival. Their technology continuing into another cycle is exactly the sort of thing the reapers are trying to prevent from happening. Prothean tech being discovered is HUGE even to a Reaper, because it means they failed at the very reason for their existence to an extent.
but that's the thing with Saren indoctrinated there was no need to fight if he hadn't gone the conduit route.
For every other cycle before us the keepers activated the relay in the citadel and before anyone knew what was happening the reapers were inside and had taken control.
The only reason it didn't happen to us was thanks to the proteans disrupting the signal to the keepers. That way they didn't activate the relay.
To correct this issue he can simply send Saren instead of the keepers. Both are perfectly fine going into the citadel council nobody will suspect anything so there is no need to fight and everything will go exactly as it did all the previous cycles.
Sovereign doesn't need to take the citadel by itself, it only needs to find a way for the citadel relay to activate.
If for whatever reason Sovereign learned about the conduit and wants to know what it is in case it's a danger to the reaper's invasion there are many other indoctrinated agents who could have done that and this would have avoided blowing up the cover of it's most important asset, Saren who has access to the citadel and the most guarded locations like the council chambers where the activation console is.
Also that a technology from the protheans exist and might be a threat might be a concern for the reapers but if the reaper's invasion starts quickly enough seeing that it prevents all the civilizations from using the relays and leaves every system isolated there is no need for concern and all the time in the world to find and destroy it while they are harvesting.
So again everything goes back to sending Saren immediately to the citadel to start the relay and new cycle.
"We were not that smart to come up with this"
As for why Sovereign needed to be present making himself vulnerable? I don't remember. Probably overriding mumbo jumbo
This of course lead to Shepard learning about the Reapers, which caused a whole chain of events, one of which is Saren getting banned from the Citadel. Being banned, he can't just walk in and trigger the Signal, especially with the console for it being in the Council Chambers.
As for why Saren didn't trigger the Signal earlier, the argument is that he simply did not receive orders to do so until after he was banned. Sovereign spent an unknown amount of time Indoctrinating Saren to do his bidding, and part of that was amassing an army of Geth and Indoctrinated followers, including Matriarch Benezia. As we saw in a cutscene later in the From Ashes DLC for ME3, the Reapers liked to use Indoctrinated agents to sow chaos and discord. This was likely mentioned in at least one of the various Codex entries too. This further reinforces the idea that Sovereign wanted to build up a power base of Indoctrinated people that he could later use to make the Reaper's war proceed smoothly. In turn, this means that Saren would not have triggered the Signal at the first opportunity he had, but instead that he would wait until Sovereign deemed it finally time.
1. Sovereign needed organic ally to use Beacons, because as Vigil said or was it implied somewhere else, can't correctly remember; they protected Beacons so only organic minds can "connect" to it and get the message. But, being that Turians/Humans are not telepathic as Protheans were, they have a hard time understanding the meaning.
2. That's why they need the "Cipher", but it's IMHO essentially just that same message or like a code to read coded messages, just spoken through a calm, connected, hive mind of a very old being (Thorian).
3. Now, why Saren couldn't just walk in the Citadel and activate the signal! So, Reapers created the Citadel and it's a big mass relay to dark space. OK! They also left Keepers to repair and maintain it and when they send them certain signal they would just active that hidden mass relay and extinction cycle would continue. OK!
But, it's never really ever said where Keepers come from or where from can that signal be activated/sent. Presumably Reapers aren't dump enough to just leave that possibility on some random console, even the one in Council Chambers.
And on top of that, even if that was possible, remember that Protheans from Ilos came to Citadel after Reapers retreated to dark space and probably not only deactivated that signal activation protocols, presumably also, locked that behind some sort of their own made protection.
And, lastly, logically, after that, Saren and Shepard needed to know how to break that protection in order to gain access to Citadel main control protocols. And they obviously downloaded/obtained/received that key/code/password/whatever from Vigil; Saren probably from archive main console or similar, forcibly for sure!
Of course, Sovereign could override any Prothean protection and just forcefully open Citadel mass relay, but he/it needed to be directly connected to Citadel as seen before last fight in ME1. Sovereign couldn't win by force alone, even with whole Geth fleet, and he/it knew it and that attack was last, desperate resort.
Without Saren's help and subsequently Shepard's intervention to stop Saren and Shepard's victory, Sovereign would still lose and Reapers would still come in ME3, just no one would even know about it until it would be totally to late!
There would be no one there to potentially stop Arrival, as no one would know what is coming!
That's explained in game, the Thorian is of an unknown age but was definitely around before the Protheans. Considering the way it interacts with living organisms, it makes sense for it to understand Prothean. It probably captured some at one point or another. The Thorian has lived through at least 2 cycles though, and it's not clear how many total. Shame you kill it really.
As for surviving the reapers, it can become dormant, and to the Reapers it may not even seem like intelligent life necessarily. Remember their goal is stopping INTELLIGENT species, I won't say more in case you haven't actually finished the series. But when you factor in what the Reapers are actually trying to achieve with the cycle, it makes sense they never killed the Thorian.