What would have been cool if ME3 went this way.

I have thought about the possibility of what if after defeating the Reapers if you find out that there are millions of more Reapers out in the galaxy, the leviathans played you for fools for they were the former species that created the Reapers yet the leviathans you see are the ones controlling everything. The reapers are independent yet the Leviathans saw it that they were the ones that stood among their synthetic counter parts. In Order to control them they harvested their organic subjects yet before they could do this they rounded up those that spoke out against this notion and turned those leviathans into harbinger and thus their first soldier was ready.

harbinger would then direct control over the Reapers and be their voice, yet the other reapers had their own prospective of things yet slowly harbinger soon regained senses and turned on the other leviathans and waged a war against their creators. After believing harbinger had its revenge Harbinger rounded up the remaining reapers and took off to another galaxy once the mass relays and citadel were completed. from there Harbinger went to other galaxy's and started to conquer them.

For over billions of years the Reapers harvested other galaxy's and then soon broke off into different sections to manage and harvest other galaxy's and Harbinger and his sector were assigned to the milky way and those galaxy's around them. However the original creators had sought to regain control of them and thus they implanted the crucible, yet the problem was that all three factions had sought to use the crucible differently. someone wanted it to destroy the reapers, the others wanted to regain control, while some believed merging with the synthetics would increase their power and control over them.

Yet all talks changed once Shepard came into the picture. They saw something in Shepard and thus backed Shepard up yet even if they didn't help Shepard they saw an opportunity and took the regaining control option. Shepard at the end of the game is occupying Harbingers time while the Leviathans get ready for work. They in turn, turn on their allies and reverse the crucible into what it was meant to do. by channeling the Reapers within the galaxy they sacrificed all the reapers functions and in turned created a different frequency that all Reapers in the universe could hear and the Leviathans regained control over them. However their former allies saw the events happened and quickly retaliated yet before they could do anything to the leviathans the citadel opened the dormant relay within and shot the leviathans into dark space were a space station for the Reapers in the section of the galaxy was at.

Therefore it leaves the galaxy to use the Reaper tech that is left over, build upon years to regain their military strength, and thus takes the fight beyond the milky way, and into a universal war and as Shepard leaves on a legacy Shepard brought hope to everyone and lived out a life in peace and it is up to the future generations/decedents to finish the fight.