Ok I hired Charon then went to do MQ, think it was after Tranquility lane or when you get captured by the president, after that he was just gone. Is there some part in the quests you will lose a companion?

you loose companion while entering vault 87, if you did then check in history museum

Followers automatically get fired then. You can try waiting a few days then go back to The Ninth Circle, he should be there waiting.