I am not convinced it is really related to travel, but in fact, there is an option if you are near Palo Alto Caltrain Station.
SamTrans (San Mateo County Transit District) offers some night buses between San Francisco (Financial District) and Palo Alto Caltrain station.
This is the line 397 that has 3 buses per night from Palo Alto Caltrain station, respaectively at 12.48, 1.48 and 2.48 am. They take 2 hours to get to San Francisco, near Mission and 1st Street.
There is an earlier possibility. You can get to the Palo Alto Transit Center or at Menlo Park Caltrain station at 11.24, 11.54 PM or 12.24 AM, and catch the ECR. You can stop at the Hillsdale Caltrain station 35 minutes later and then catch the 292 towards San Francisco Financial District. There will be a (maybe tight) connection at Hillsdale station as the 292 leaves at 12.05 and 1.05 AM. It arrives 1h30 later.
There might be some other possible connection (there are a lot of different transit authorities in the area).