Where do we come from? It's something that's been asked by man for millennia and prominent in all manner of media (its the grounding of religion). Now, thanks to centuries of scientific advancement, we know about evolution by natural selection and the basic origins of all Earth based life. Where basic life itself came from is still unknown, but science will keep working on it. Don't let that stop sci-fi from presenting interesting spins on how it happened. The most prominent is 2001: A Space Odyssey, which chalked up major advancements in human evolution to some external alien involvement greater than our comprehension, but recently things have been getting even more unbelievable; Prometheus threw science to the wind and presented the idea that we are the product of experimentation by some alien beings, to mixed reaction. And it doesn't need to be as far back as the origins of man. More recent historical meddling is necessary for just about every period sci-fi; according to X-Men mutants have been shaping history for decades. Transformers has recently decided to straddle both aspects of the sub-genre; it has defined its whole existence by having the Cybertronians pop up at all points of Earth's development, with the latest, Age Of Extinction, not only messing with the extinction of the dinosaurs, but also turning the spotlight on the robots in disguise's origins.
