Apparently, depending on other factors, Swanson can just disappear too.
At the end of the mission where you rescue Captain Monroe from being charged with treason, there's a scene that is different depending on whether you did a certain stranger quest. In my game I met up with the nun, who was boarding a train to Mexico. If you don't meet up with the nun, you meet with Swanson instead as he's boarding the train to NY. ---
