So, in Control, Shepard becomes a Human-Reaper and starts mass murdering people?
So, in Synthesis, Shepard becomes a Human-Reaper?
EDI as well.
This was actually foreshadowed quite well in the previous games.
EDI (ME2): Reapers are sapient constructs. A hybrid of organic and inorganic material. They may be facilitating the Reaper equivalent of reproduction.
EDI (ME3): As the line between synthetic and organic disappears, we may transcend mortality itself.
Harbinger (ME2): Thank us, beg us for immortality.
EDI (ME3): To reach a level of existence I cannot even imagine.
Harbinger (ME2): Your species will razed to a new existence. That which you know as Reapers are your salvation through destruction.
Shepard: Eternal, immortal, infinite
Saren: We are the pinnacle of creation. Immortal, infallible, perfect. (in a Reaper voice, like Shepard)
Shepard: I will destroy those who threaten the future of the many
In ME1, the Reapers are referred to as Legion. In ME3, they refer to themselves as Many. It essentially means the same thing. A very large indefinite number.
Anyone who tries to destroy the Reapers (the galaxy which you helped forge all those alliances to help destroy the Reapers) will be destroyed themselves. Shepard essentially switched sides and is now working as an agent of the Reapers under their control. Not as the savior of the galaxy you thought he was.