Board Thread:Metal Gear Solid V/@comment-26523073-20150623001037/@comment-21823483-20151122090949

Eh, I'll chalk it to John and Adam being close friends. Also Big Boss wanted nothing to do with the orginization (between Zero's lies, him being made the icon and the LET project/ his clones) he left and pursued his own interpretatios of The Boss's will (Peace Walker), in MGSV, he's busy building Outer Heaven while Venom and Diamond Dogs have the world stage. Ocelot says this in the ening conversation with Miller.

So John being in a Patriot HQ during this time would be odd (though he returns to FOXHOUND to draw attention from Outer Heaven as he hands over leadership to Venom as Diamond Dogs moved to there.)