Beverly Scott abruptly quit as general manager of the Massachusetts Bay Transportation Authority, the storm-besieged agency that operates the Greater Boston subway and commuter rail system.

Scott, 63, resigned late Wednesday shortly after the board of the state Department of Transportation, which oversees the MBTA, unanimously gave her a vote of confidence. She will remain until April 11 and assist in the transition, she said in a letter to board chairman John Jenkins.

Twice in the past two weeks, the MBTA had to shut down service for more than a day after three storms dumped as many as 80 inches of snow in some parts of the state. Trains were stuck between outdoor stations and riders left freezing on platforms.

Gov. Charlie Baker, who took office in January, has criticized the operations of the "T," as locals call the system. On Wednesday, however, Baker said Scott's resignation stunned him.

"It was certainly a surprise to me," he told reporters.

One day earlier, Scott said during a highly animated news conference that she wouldn't resign. "Do you know what? I'm not even getting into those conversations," she said.

The MBTA is the country's oldest transit system and a large municipal bond issuer.

"Oh Lord Jesus," said she Tuesday when reminded of the T's $19 billion of debt. "The T got stuck with all this Big Dig debt from years ago."

According to Scott, the T had to absorb $3.5 billion in debt related to the Big Dig megaproject, the Central Artery/Tunnel Project .

Before arriving at the MBTA in December 2012, Scott was chief executive and general manager of the Metropolitan Atlanta Rapid Transit Authority. She also held senior-level positions at several other agencies, including New York's Metropolitan Transportation Authority and the Rhode Island Public Transit Authority, where she also served as general manager.

On Thursday, state Rep. Raymond Hull, D-Providence, asked Rhode Island Gov. Gina Raimondo to offer the RIPTA job to Scott. "One state's loss can be our state's gain," said Hull.

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