BUS or TRAIN + METRO
From Malpensa airport the bus is the best choice to reach Milan:
in the airport follow the signs to buses, which are just in the front of the right exit,
and take one to Milano Stazione Centrale (Central railways station).
The way took about 50 minutes, for 9 euro each person.
From Malpensa, the last bus is at 00:45 am, after you can reach the apartment only by taxi, for 95 euros flat.
An option, a little more expensive and a little less pratic is the train:
take the Malpensa Express to Milano Stazione Centrale (Central railways station) (not to Garibaldi FS).
The apartment is straightforward to reach with metro: go in the green line metro station, just in the front of railways station, and bring the train to Loreto, at Loreto bring the red metro line to Villa S. Giovanni. 20 minutes for the entire trip.
The last metro train departs about at 00:15 am, after you can reach the apartment only by taxi for about 20 euros.
