John finds out that Ronon and Rodney occasionally hook up, because sex. Neither of them has any sexuality hang ups. John gets jealous. He's still in the closet, even with the repeal of DADT, because of so many years of hiding, of occasional, furtive backroom hookups while on leave. Maybe also because of his dad? (but not necessary).

It can be funny or angsty or anything in between, but HEA please and McShep end game. :)