I would also not expect any bad guy to show.
I think it's a story about. Like repairing things that once been broken, or bonds in this case. Like kintsugi.
My theory is life simply got in the way of Kyou and MC. Her family broken up, she dropped out of school. With her more livelier outlook, she moved on and eventually met with Minori's dad. But once again, life happened, making Minori her last family member. For MC, with more brooding look, he also moved on somewhat (we saw him being productive in general: cooking, painting, making a living out of his craft), but still could not forget Kyou. Now both of them have the chance to mend their broken bond.