The door banging opening, well that wasn't necessarily the act of someone who was entering into this place, wherever this place was, with intention of doing harm. Maybe the wind had taken the door, or, well there could have been a lot of reasons. Deciding it was better to be safe, than sorry, John ducked down behind a table.
Even in a house that was run like the Connor household currently was, one didn't got to the bathroom armed. So ducking behind the table, John tried to assess the situation, and see if there was a weapon handy. Because looking up from behind the table he was seeking refuge behind, he could see that the other had a weapon of someone sort.