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In my opinion what is going on is that............Shepard went into an "unconscious state-like dream" since Shephard went up the POWERFUL LIGHT BEAM that caused it. Then it's harbinger/Reaper trying to "indoctrinate-hack," Shepard. When you choose the ending "destroy the reapers," what your really doing is  trying to "break free of the indoctrination /hack." Hence why the Catalyst was in the form of the little boy from Earth  aka "little boy A.I" and LIED that all synthetics will die including Shepard, but disappeared as soon as Shepard decided to choose destroy the Reaper ending. That's why this is the only ending where Shephard lives. The part when Shepard "breaths," means he awakens from the "unconscious state-like dream," successfully bypassing the hack.