The country’s second-largest rail system had been open for barely 20 minutes Thursday morning when Metro experienced yet another breakdown in a seemingly endless series of breakdowns. This time, a train preparing to begin service at the Smithsonian station derailed, forcing Metro officials to halt operations on portions of three lines and to shut down two stations.

The move left thousands of angry, frustrated commuters on the Blue, Orange and Silver lines scrambling for alternate ways to navigate the region — and howling over the latest incident to plague the troubled system.

The Federal Triangle and Smithsonian stations reopened around 8 p.m., and trains were servicing those stations. Single tracking continued.

No passengers were aboard the train and no injuries were reported in the derailment. Officials were able to restore partial service in time for the evening commute on the Blue and Orange lines, but that was of little comfort to tens of thousands of Metro customers who still faced long delays for the ride home. Silver Line trains were only running between Wiehle-Reston East and East Falls Church as of Thursday evening.

“It’s too expensive and there’s always something wrong,” said Erica Fisher, 25, echoing a complaint uttered by many riders over the past few months.

Metro officials were contrite.

“We know this is a great inconvenience to our passengers, but we are doing our best to resolve the situation,” said Jack Requa, Metro’s interim general manager. “We have to know what happened so we can prevent it from happening again.”

The apology from Metro officials has become all too familiar. In May, an electrical malfunction and smoke in a Metro tunnel under the Potomac caused an hours-long suspension of service on a bottleneck stretch of the same three rail lines. And Metro is under federal investigation after a passenger died following a smoke incident on the Yellow line in January.

Thursday’s incident began about 5:20 a.m. when three cars on a six-car train went off the tracks inside a tunnel between the Smithsonian and Federal Triangle stations as the operator was moving it into position to begin morning service at Smithsonian. The cause of the derailment is still under investigation.

Crews worked throughout the day to “re-rail” the train, a process that involves moving the wheels back onto the tracks using jacks and other heavy equipment. But the task was complicated because the derailment occurred inside a tunnel, according to Metro spokesman Dan Stessel. About 2 p.m., officials announced that crews were able to remove two of the four cars, enabling Metro to offer limited service.

Requa briefed board members on the incident at a previously scheduled special meeting that had been called to deal with two other pressing Metro matters: acceptance of the Silver Spring Transit Center and review and acceptance of a 2014 financial audit that is more than 10 months overdue. The board voted to give Requa the go-ahead to take control of the Silver Spring Transit Center, the troubled transit project that is four years late and $50 million overbudget. It also reviewed and accepted the result of the 2014 financial audit. But the latest breakdown overshadowed all other Metro business.

Metro has suspended service on the Orange, Silver and Blue lines between the McPherson Square and Federal Center SW stations after a train with no passengers derailed at Smithsonian station. (WUSA9)

“It is a terrible disappointment when something like this happens,” said board chairman Mortimer Downey when asked about Thursday morning’s derailment.

Morning mess

The derailment affected two of Metro’s main transfer points, L’Enfant and Metro Center, forcing many passengers onto crowded shuttle buses.

Many riders said they got little or no information from the transit agency about the problem. Even though some station managers had bullhorns as they were directing passengers, some riders said they couldn’t hear announcements about what was going on or where to go.

“It’s absolutely horrible,” said Sam Kingston, 35. After 90 minutes in the Metro system, he was only halfway to his job in Rosslyn from his home near the Suitland stop.

For Courtney Klein, her normal 30-minute commute from the Rosslyn stop to her internship at a technology firm near Capitol Hill took nearly two hours.

Metro offered free bus rides for passengers affected by the messy morning commute, and it dispatched more than 50 free shuttle buses to the impacted stops. It pledged to run buses for those needing to get to the two closed stations in the afternoon as well.

The incident added to Metro’s list of reliability issues. It came a day after service was suspended twice at the busy Bethesda stop on Metro’s Red Line after a new escalator went out of service and then a power outage at the stop.

“While the cause of the derailment is still unknown, today’s Metro incident is yet another example of why we must retire and replace the old series rail cars and make immediate system and safety upgrades,” said Rep. Gerald E. Connolly (D-Va.)

Officials at Metro said the train may have derailed because of a problem at an interlocking, an area of track that has signals and switches and helps trains move from one track to another, between the Federal Triangle and Smithsonian stations.

Metro officials emphasized, however, that they’re still not certain. They think the damage to that area is minor, but once the train is removed the tracks will be inspected before full service is restarted.

The train was performing what is considered a routine daily move.

It left the New Carrollton rail yard shortly after the system opened at 5 a.m. It was headed west, but was going to switch over to the eastbound track near the Federal Triangle stop and pick up its first passengers of the day at the Smithsonian station.

The train began to derail as it was moving through the interlocking . Three cars of the train, made up of several of the system’s oldest 1000- and 2000-series rail cars, went off the track. Requa said the rail cars did not tip over and that the wheels landed about a foot from the tracks.

The operator of the train is undergoing drug and alcohol testing, which are routine Metro procedures in an incident such as this one, officials said.

Officials said they had reported the incident to officials at two safety oversight bodies — the National Transportation Safety Board and the Tri-State Oversight Commission — both of which are considered watchdogs of the quasi-public transit agency.

Metro has had other problems with trains derailing.

In 2013, a Red Line train derailed near the Rhode Island Avenue stop as it was being moved from one rail yard to another for maintenance. No one was injured and no passengers were on it at the time. And in 2012, a train with about 1,000 riders on it derailed at the Rosslyn stop. No one was injured. That incident, Metro has said, was most likely the result of human error.

Elizabeth Koh, Luz Lazo, Faiz Siddiqui and Julie Zauzmer contributed to this report.