There have been a few suggestions which were along the lines of "Space Hitler wanted to be alone in the galaxy and so killed everyone else". That's pretty obvious to me, so how about instead...
Your survivor was a soldier who was supposed to stop Space Hitler. They were just a moment too late.
Space Hitler (SH from here on) comes up with a genius plan to eradicate all life in the galaxy, for reasons that we may never comprehend. He engineers not one, but several deadly plagues for each of the inhabited worlds in our galaxy, and to ensure no survivors, the plagues are delivered from orbit by robots that will descend on the few survivors the plague cocktails leave behind.
Our survivor to be, let's call them Anne, is a part of the strike team that's sent to stop SH in his secret base, hidden inside of one of the moons of a gas giant. Her team is the best, led by amazing strategists, armed to the teeth, but SH expected this strike team so the moon base's defenses are just as devastating. Each line of defense claims 2-5 soldiers, but they manage to make progress.
There are multiple possible entry points to SH's control room, where he waits for all of his death machines to be in position to commence the galactic devastation he's spent years planning. It just so happens that Anne's air vent was the only entry point that turned out to be breachable. She lands on the floor just as SH presses his big red button, and shoots her laser blaster through his skull... But it's too late. The plagues have been deployed, and there's no going back now.
SH had planned to rebuild society as he wanted, so he already has a lot of equipment in his moon base for this, and plans of where to start. But first comes the waiting. With deadly plagues ravaging all inhabited worlds, the only solution is to quarantine them, waiting for the pathogens to die out by themselves.
Ten, twenty, fifty years pass. The once young and lively soldier Anne is now slow and wise. Over these decades, she's had time to investigate each planet's seed banks and genetic samples and now has a plan to rebuild the galaxy as they once were. The robots, once full of death and pain, now carry hope. The only hope for the future of the galaxy. Now, all Anne needs to do is to press that big red button...