This is the exact description from HAL's site. And I am taking it on Saturday, June 3rd. Gives a departure time of 8:15 am and that is all. I have scoured the internet, chat boards, and facebook groups to find someone who has actually taken this excursion so I can get actual times to and from the S. Pietro station with no luck.
On Your Own: Rome by Train
It consists of a motorcoach ride from the ship to the railway station in Civitavecchia and a 60-minute train ride to the Vatican City's St Peter's Station. The train coach escort will advise you of the pick-up time for the return journey. You will have approximately 6½ hours to shop and explore independently in the Vatican and in Rome. A city map is provided and public transportation in Rome is readily available.
Optional upgrade: You can maximize your day in Rome with a hop-on, hop-off bus ticket. Purchase the upgrade on the train journey to Rome (when available). The hop-on, hop-off bus stops at many of the main archaeological sites and historical landmarks. The buses run continuously arriving at each stop about every 20 to 30 minutes.
Bring local currency for attractions, meals and shopping, as many vendors do not accept credit cards or US dollars.