Someone already mentioned Regensburg - there's a direct Regional train from MUC Airport Station to Regensburg. For a very chill day trip, I would recommend Freising as well. Direct bus, or the aforementioned regional train - it makes a stop in Freising on the way to Regensburg. Freising is small, but very historical. World's largest continuously operating brewery, Weihenstephan, is on a hill, and on another hill is the cathedral, which is absolutely stunning inside. It may not keep you occupied for your full 12 hours, but at least you won't be rushing to get to or from the airport.

If you do decide for Freising, give me a shout, I'll recommend some good cafes and places to eat, I spent several months there some time ago