My first reaction was 'weasel'. They can get through some pretty small spaces. Whatever it was got in somehow, so you need to figure that out, it may very well come back. Look for areas of chewing, digging, bent wire, scratch marks, it likely left some kind of evidence behind. Check for loose wire on all openings. Check the floor under the raised part of the coop. Think like a very determined predator while looking for how it got in. Your rooster may have tried to defend the hens and gave good enough to run it off this time. If you can borrow or set up a game camera that may help identify what it is and how it's getting in, or if the ground around your coop is flat enough spreading flour or cornstarch may pick up some prints you can identify. I suppose it's even possible that it got in before the door closed, so maybe close them up a little earlier and make sure they are the only occupants until you figure it out. And some pictures of your coop and set up might help, someone may see something you've missed, it's easy to do.
I'm very sorry you lost him, I'm always sad to lose a good roo.
It still will likely come back and try again, so watch for signs.
