The Indoctrination Theory is desperate attempt by fans to make sense of a terrible ending. It's a nice theory but Mac Walters and Casey Hudson wanted to vague ending that promoted speculation. Despite promising several times in multiple interviews that ME3 would provide closure and have multiple endings for the various Shepard's created by fans of the series. Causing a series of chain reaction supernovas, Arrival establishes that an exploding relay hits with the force of supernova, pretty much wipes out most of the life in the Milky Way.