Rei leaving his home thinking it’s the only way to protect Kazuki and Miri (after all, papas are supposed to protect you). It’s better this way.
He leaves most of the “shared things” - exercise equipment, plants, kid-friendly games and all his gaming gear, along with a simple “Thank you, for everything,” note.
Kazuki, thinking he really did just go back to his dad for the organization because that’s what Boss wanted. Plus, Rei was getting (sick and) tired of playing house with him and a kid he adopted on a whim, right?
He’s torn - how much of his feelings are his own and how much are Miri’s? Can he continue like this, with just himself?
Then Kazuki visiting Kyu after a few days getting settled being a single parent and coming up with ways to explain it to Miri, only to have Kyu seemed surprised he didn’t know that Rei left to ensure his and Miri’s safety.
(Kyu is also holding on to a box of stuff Rei couldn’t bring to the Boss’s place after Rei asked him for advice on how to rent storage units. For a single box.)
Kyu hands Kazuki an envelope Rei had left for him. It contains a single photo, with “I wish we had more time” written on the back in Rei’s handwriting.