War. The reapers become aware of their strength and either band together to rule the galaxy, exterminating all resistance, or form petty kingdoms from the ashes utilising slave races as resource.
And those who have been forced into this situation by an idiot called shepard curse the name for the remainder of their short, miserable lives.
Oh, are we doing random extremely pessimistic worst case scenarios now? Okay I'll join in. I'll do one for high ems destroy:
Shepard lies on the wreckage of the citadel, fatally injured, waiting for help, that finally arrvives too late. All the search team can do is recover Shepards dead, broken body. The relay system is destroyed and the races of the galaxy try to repair it, but after soon they start to realize, that without the help of the Reapers they lack the knowledge and resources to actually do that. All attempts to repair the citadel or the relay network fail ultimately.
The single systems are isolated from one another. Economy (which was already low to begin with after the war) completely collapses. Resources are getting scarce. The turians and Quarians on earth are the first to starve. The Quarians left on Rannoch (If there are any left) are unable to adjust to life on the planet without the Geth or imported goods from the rest of the galaxy and soon enough the entire species is wiped out by diseases and starvation.
Because most of the Turian military died on earth Palaven descends into chaos and despair. Cities burn, people die and the Turian civilisation falls back into a dark age. Thessia is never able to recover from the blow the Reapers delivered to it and is thrown back to the status of a third world country. The Asari are cut of from the rest of the galaxy and the number of Ardart Yakshi significantly increases. Soon society breaks apart into rivalising tribes that worship the Ardat Yakshi as gods of death.
On earth Hackett tries to keep things stable. But the entire planet lies in ruins, the infastructure is almost destroyed and food becomes more scarce by the day. Hackett is eventually assassinated and anarchy breaks loose. Various warlords rise to take over the planet and the entire globe is enguled by total war once again. It ultimately peaks in a devastating nuclear fallout that renders the planet a desolate wasteland. The few surviving humans live without hope and joy.
50 years in the future the last living human being looks up to the stars with tears in her eyes and curses Shepards name. Then she shoots herself.
See, that's what happens if you choose destroy. You monsters 
Just kidding (mostly). Don't come after me with your pitchforks Destroyers.