It was all about the semi-magic of the Mass Effect, ie, the mysterious and ancient Mass Relays. It was even in the TITLE. As civilizations grew up and started using the relays, the dark energy buildup from their use started to swell. Because of that, there was a failsafe: at a certain point, the higher dark energy levels would set off the Reapers to attack and destroy the civilized societies. Otherwise, the suns would go out.
The final decision, I read, was for Shepard to destroy the Reapers, trusting the current cycle to figure out a way to stop the dark energy buildup in the galaxy... or sacrifice all of humanity to fix the problem once and for all.