I just had this wild theory in my head. I believe the Mass Effect series will culminate with a dark plot twist: Shepard will turn to the dark side and ultimately join the Reapers. Let me explain how.
There was a thread here not too long ago saying that Shepard is already becoming another Saren. In order to resurrect Shepard, Cerberus had to use cybernetic implants. During the course of the game you can research a lot of Shepard's personal upgrades, so by the end of ME2 he/she is already half-machine/half-human. You are a rogue Spectre working for a terrorist organization and you have armies of Geth, Krogan, and even Rachni at your disposal. I'll take another step further and say that Shepard is on his/her way to becoming the perfect agent and weapon for the Reapers.
I found it weird that while every organic species who have come in contact with a Reaper suffered the effects of indoctrination, Shepard & crew were apparently immune. Perhaps Shepard is also suffering from indoctrination but at very subtle levels. Remember Saren? He said that as indoctrination becomes stronger, the subject becomes more mindless and useless. That's why Sovereign let Saren retain most of his free will. Shepard has encountered not ONE, but TWO reapers by the end of ME2 (Sovereign + derelict Reaper). A normal human would have already become a mindless husk, but Shepard is largely untouched. Maybe the Reapers have a plan for him/her...
Maybe at the start of ME3 we will see Shepard's sanity erode by the indoctrination. To further push that point the writers could add that Shepard's love interest is accidently killed or disappeared by the Citadel species. This becomes the last straw, and at that moment Shepard loses his/her mind completely and all traces of humanity. Shepard puts the blame on all organics, and decides to take revenge by manually opening the Citadel's relay (normally only a Reaper can do that, but Shepard has gathered enough knowledge during his/her travels, perhaps obtained from the derelict Reaper or from the Collector base).
And the Reapers finally win not with Geth armies nor Collector armies, but through the man that was once considered to be the Galaxy's savior. A very dark and ironic ending.





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