I base off a mixture of pre-existing tropes and work from there. I may follow a formula I already enjoy or throw in some unexpected twists, but I always start by combining 2-3 tropes such as "magical girls, smart-dumb pair, GL" and then build a story.
I know of one manga artist who actually plays a game where she flips through a dictionary and lands on 3 words, then must make a short one-shot based on those words!