In Blue Ending Sheapard could pull a Revan: one day dissappear with the rest of the Reapers, pursuing some unknown quest. Without any word of warning or explanation.
Lack of Reaper police force would reinvigorate all the old conflicts of the galaxy, which is still licking its wounds after the last great war.
Protagonists of the game would travel through the many systems, solving minor conflicts and gathering clues to establish where Shepard went and why, in hope that his return would stop the galaxy from tearing itself apart.
In the end they would learn that Shepard is not coming back anytime soon. Together with the Reaper fleet he's facing a new threat from beyond the Milky Way, once again protecting the galaxy with his life. And he is slowly loosing the battle. So in the second part of the trilogy the crew would become major peacekeers, trying to sort out any problems and unite all forces before the coming storm.
Third part would tell the story of the final confrontation with the Unknown Threat, together with the remnant of the Reaper fleet. And there Shepard (who could, in some form, become a party member, albeit not directly controlled) would meet his last and final, heroic death.
