The “safe” part entails state-of-the-art features turning the traditional “dead man’s switch” into technological wizardry. The engineer must activate a safety switch every 45 seconds or the train comes to a controlled stop. Sensors on the train monitor track conditions ahead, and automatically enforce speed-compliance. The engineer can run the train slower than the legal limit, but never faster; and sensors will detect obstacles ahead before the human eye can see them.

The “secret” part is that despite having been built with safety features no other Greater Boston commuter line has, two of the Old Colony branches -- Greenbush and Plymouth/Kingston -- lost their weekend service on July 1.

At six-foot-seven, Prone would have a hard time hiding in plain sight under the best of circumstances. At South Station, colleagues from his 40 years on the rails greet him like a returning Olympian. In a darkened room the size of an auditorium on the top floor of South Station, he introduces me to Richard Murphy, Mass. Bay Commuter Rail’s chief train dispatcher. This is the control room for all commuter trains out of South Station and all Amtrak trains as far as New Haven and Worcester.

The only word that matters here is safety. While I am mutely observing, a person is reported trespassing on the tracks in Stoughton. Police quickly have the man in custody, but Murphy directs that trains not move until police at the scene officially confirm it. One imagines passengers looking about, seeing nothing -- grumbling. In ten minutes it’s over. There will be no rush of media to Stoughton, because there will be no story. Safety has prevailed.

The engineer who will run the locomotive to Kingston is friendly and relaxed, as those who do dangerous jobs need to be. He puts an iced coffee down where he will be able to reach it, with a joke about how much he has spilled over the years. He advises me to hold on as I step back onto the platform. He’s not joking. I tell him I know about holding on from boats.

The locomotive is a rebuilt 40-year-old Canadian National engine with duct tape keeping the vinyl ceiling from reaching its preferred destination -- the top of the engineer’s head. But that is deceptive. This locomotive has all the safety features required by a Federal Railroad Administration “Class-IV Railroad,” allowing speeds of 80 mph for passenger service and 50 mph for freight on the Plymouth/Kingston and Middleboro/Lakeville branches. (The Greenbush branch is a Class-III Railroad, with top speeds of 60 and 40.)

With all the best safety features, Plymouth/Kingston and Middleboro/Lakeville opened for service in 1997. Within a few years the millions of concrete ties that had been installed beneath the 135-pound per-yard welded concrete rail turned out to be defective. Service on the new lines had to be curtailed while the concrete ties were replaced with West Virginia oak, which give a smoother ride than concrete. (Concrete ties are used in Europe because of a shortage of trees; their use in the United States, where oak forests are plentiful, is an affectation.)

Two years of replacing the ties on our state-of-the-art branches naturally caused a fall-off in ridership. It was then that the MBTA’s financial problems led to the ridership surveys that led to the elimination of weekend service on the Plymouth/Kingston and Greenbush branches. (Weekend service continues on the Middleboro/Lakeville branch.)

After a 25-year campaign by business and political leaders, a huge investment was made to create the safest commuter rail operation in the United States. Yet after 15 years of operation, it is allowed to be a well-kept secret, with no weekend service on two of the branches, including the one that has been in service for just five years.