I just saw this theory on Reapers over at the BSN, and it actually makes a twisted kind of sense. I wanted to see what everyone else thought.
I'm copy/pasting the text straight from the post for the BSN (and link) phobic. I'm not altering any of the poster's grammar or spelling.
"First of all, I need to go over everything we know about the Reapers, starting with ME1.
In ME1, we meet Sovereign, a Reaper. Sovereign is a 2km long dreadnought-class starship of great destructive and defensive capacity, capable of bending the minds of organic beings to his will through indoctrination and create organic-Reaper hybrids (majority being mindless husks) by injecting Reaper technology into their bodies (majority via dragon's teeth). At the end, after Saren - his indoctrinated and heavily modified agent - is killed, Sovereign assumes control of the extensive Reaper cybernetics in his body. When husk-Saren is killed, Sovereign seemingly "powers down", allowing the fleets to destroy him.
In ME2, we meet Harbinger, another Reaper. Harbinger is presumably of the same classification as Sovereign, with the same destructive and defensive capacity and other abilities. As we learn late in the game, Harbinger is actually with the Reaper fleet outside the galaxy, directing the Collector General through what is believed to be some kind of quantum entanglement technology. The General acts like a conduit for Harbinger, allowing him to assume control of basic Collector units anywhere in the galaxy to engage enemies like Shepard in firefights personally, establishing a "control hierarchy", more extensive than what we saw in ME1 with Saren and Sovereign. We also learn that the Collectors, under Harbinger's direction, are kidnapping humans to use their genetic material to build a new Reaper, and that Harbinger is interested in obtaining Shepard's body.
Also in ME2, we meet Legion, who tells us that Sovereign - actually referring to itself as Nazara - is actually a myriad of AI processes, much like the geth are.
Now, for me, the very end of ME2 is where it all gets funky. The incomplete human-reaper, despite trying to actively kill Shepard, shows no sign of actual intelligence or sapience, much unlike the other Reapers who possess the capacity for advanced thought and speech. Now, one could argue that the human-reaper's incomplete state is to blame, but then again, machines cannot "mature" the way we do. It acts more like a mindless mech than a creature with a will of it's own.
But then, we take a look back at the derelict Reaper. This is a complete Reaper, but one that has been destroyed by a particularly nasty, planet-based mass cannon. Despite showing no signs of activity like the other mature Reapers, the derelict Reaper can still indoctrinate and affect on-board systems.
Now, there is not much basis for this, but what if the Reapers - their ship forms - are just another form of shells for the actual Reapers to assume control of? Let's think about it. Harbinger has shown us that the "Assuming Control"-part works in layers - he controlled the Collector General, and through the General he could control the basic Collectors. What if the Reaper ships (and in ME3, the Reaper scarabs) are just another layer in this hierarchy of control?
Now, this next part has no real basis either, but I believe it is worth mentioning. I have long suspected that the twin relay to the Citadel Relay, out in dark space, is actually a gigantic "mothership" and an ansible hub for Reaper communication with each other and with their agents in the galaxy. It's basically a mobile HQ where the Reapers organize their invasions, and where all ships dock between cycles.
Let's go back to Harbinger's interest in Shepard. At first glance, you would assume Harbinger wants Shepard so he can goo him down to Reaper mortar. But Shepard's really just one man, and what kind of significant difference could Shepard do in the grand scheme of building a new Reaper? It would just be better to kill him off and be done with it.
Since we've established the possibility that the Reaper ships are just another layer in the control hierarchy, what if the Harbinger wants Shepard as a control unit for the Human-Reaper, in order to give it the intelligence and sapience exhibited by all the other Reapers?
Going with the idea the Dark Space Relay is a mobile HQ for the Reapers and that the Reaper ships are just shells to be controlled, this would indicate that the "real" Reapers are housed aboard this massive HQ superstructure, using it's ansible to transfer their consciousness into the Reaper ships and direct invasions personally. This protects them from actual harm, and the "death" of one vessel does not compromise the overall network.
But what are the real Reapers, then? Well, my belief is that they are first and foremost members of the original Reaper species, but also the heroes of conquered civilizations - people of indomitable mind, body and spirit who through their actions have earned the respect and admiration of the Reapers - who were captured, infused with and brainwashed by Reaper technology, and then connected into a massive neural network of minds sharing thoughts freely between every and all Reaper control units, vessels, artifacts and the Reaper HQ itself. The "hero" is then given a dreadnought shell to possess - created from his or her own species - which will serve as his or her new bodily vessel in service to the Reapers.
What makes me believe this is because Legion says Reapers are basically a multitude of AI processes working in unison, much like the geth. Now, I am not saying that Legion is lying, but considering that both Sovereign and Harbinger refer to themselves as "I" as opposed to "We", it implies that these processes are not in charge of the ship, but are directed by a singular consciousness. Since we know that Reapers take control of their pawns via Reaper cybernetics (Saren in ME1, who was extensively modified, and the Collectors in ME2, who had tech instead of organs), I believe the Reapers assume control of these AI processes in the ship in order to control the ship itself. Without the control unit, the AI processes cannot do much more than maintain the ship's internal systems.
Even Reapers who fail or have their vessels destroyed, like the derelict Reaper and Sovereign, retain their worth in the network. I suspect that this is what happened to Sovereign at the end of ME1. When it became clear he was unable to stop Shepard from preventing the invasion with husk-Saren and that his vessel was pretty much doomed from the massive barrage pounding away at his shields, he released control which in turn allowed the galactic fleets to destroy his vessel, conveniently scattering Reaper technology everywhere for shady organizations *coughcerberuscough* to collect. As the Reapers are still part of the network, they can continue to exert the effect of indoctrination upon those examining the remains of their vessels, as in the case of the derelict Reaper and possibly Sovereign as well.
So, what does this tell us?
Basically, if my theory is correct, we will have to travel to the Reaper HQ in dark space in ME3 and blow it to hell in order to defeat them. Destroying the HQ will destroy the neural network and the Reaper users, rendering every single remaining ship defunct as well as permanently eliminating the effect of indoctrination from Reaper technology." (
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