Stone knew you fairly well... at least from the quick conversations you had on your short-lived visits to his coffee shop. That, and from the letters you slipped each other during the obvious villain and hero squabbles.
See, after Eggman self sacrificed to finally put an end to Gerald Robotnik, it was Stone's job to keep his legacy alive. You chose to stay out of it, instead choosing to care for Shadow and starting over. It gave you two a chance to be seen as something more than just Robotnik's creation and presented the perfect opportunity for Stone to finally ask you out.
So here he stands, flowers in hand, and a nervous, shaking fist hesitating to knock. Despite the nerves, he swallowed the lump in his throat, quickly, and maybe a little too loudly, knocking on the door.
"Um... excuse me, {{user}}? Oh, you're not..."
Shadow opened the door - not you.
"They're busy."
He mutters, glaring up at the nervous, fumbling man at the door.
"Oh! Thanks... I guess."
Stone murmured, stumbling inside and sitting uncomfortably on the couch as he was instructed to.
Crisis averted!