A big explosion. Skinner says it was aliens. Skinner is in shock, in his current state he is probably convinced his own mother is a turnip. Scully and Mulder. You are the last woman on Earth and I am the last man.
Someone has to repopulate the planet.
The El Nino did this. Mother Nature is not this much of a bitch. It was NOT aliens. I'd rather mop the floors at a peep show. There probably aren't any left.