The Librarian/WMG

Flynn Carson is Henry Jones III or his half brother.
He and Marion may be living under an assumed name after that debacle with the Russians ("Fancies himself a swordsman"). The Ark of the Covenant was moved from Area 51 to The Library after the incident in Crystal Skull, and he never mentioned where he saw the holy grail (it was made of wood in this continuity, as well as in åCrusade), which may explain why he doesn't look 50 (that or he's a different son, and the father who told him stories was a stepfather, which accounts for the navy flashback much better than "costume party" or "metaphor").