Shepard chose to destroy Sovereign. The Council then declared war on the SA for that betrayal. The Humans tried to fight but it was a losing battle. Subjugation leading to extinction was not acceptable for making the hard military decision so the Humans chose another path and made a deal with the Reapers. The galaxy and the Cycle would never be the same. AU Shepard says obey

[AU] The Illusive Man said that salvation comes with a cost. When corruption seeps into the galaxy, when centuries of status quo suddenly breaks in a mere decade, when blood's spilled among the stars like never before, when extinction looms over civilization, when morality is merely a shade... salvation can only come with sacrifice. [AU First Contact War & Reaper War; GRAPHIC]

A house divided cannot stand. Following an explosive first contact, and the cementation of their place as a galactic superpower, the Systems Alliance must now deal with the consequences of their choices and the aftermath of their wars. Earth is set ablaze, Sparta is torn apart, and below it all simmers an ancient, apocalyptic plot. The finale to the WarVerse Prequel Wars trilogy.