In a move that surprised Beacon Hill, the newly controversial general manager of the MBTA,  Beverly Scott, submitted her letter of resignation Tuesday.

Scott said that she will step down in 60 days, and that she's looking forward to spending quality time with her family.  

The letter made only parenthetical reference to the punishing snow that has hit the region. And it made no reference to the political storm that swirled around her ever since Governor Charlie Baker said he was  "disappointed" in recent T performance, which he termed "unacceptable".

Three big storms in two weeks taxed the capabilities of the transit authority -- especially its rail services: trolleys, commuter trains, and subways. It is, most knowledgeable with the situation agree,  a complicated problem. But, simply put, opinion divides into two camps: those who see the biggest issue as lack of investment in aging equipment and tracks, and those who point to union featherbedding as obstructing cost-effective management. 

Scott submitted her letter just hours after the Department of Transportation Board gave her a unanimous vote of confidence.

The board was "stunned" by the announcement, according to John Jenkins of the MassDOT Board of Directors.

"Be clear, this Board has had no discussions at any time about her tenure as General Manager.  We hoped and expected that she would fulfill her three-year contract, which ends in December of this year," he said in a statement.

In retrospect, Tuesday's board meeting had some aspects of a carefully choreographed affair.

The meeting began with public comments from transportation advocates and community members, who almost unanimously praised Scott, who looked on appreciatively as they addressed the board.

“I think it’s unfair that Dr. Scott has to face questions about her future.

 And we hope that we’re able to work with Dr. Scott.

And I don’t know where this is coming from and how much is being whipped up by the media, but we must prevent any scapegoating.

It’s not her fault it snowed here.

 I don’t envy her, but I’m certainly glad to have her at the helm of the MBTA.

I think this is the kind of tough and reasonable leader that we need for a tough and unreasonable job.”

In a show of seemingly unequivocal support, the state’s Secretary of Transportation, Stephanie Pollack, said the Baker administration had no plans, desire or ability to change leadership at the MBTA. And she said they recognize her hard to deal with the impact of the crippling storm.

“We intend to work with the existing leadership, with Dr. Scott and with this board to identify and solve the problems that have led to the system’s failure in recent weeks. As well as to develop detailed operational and maintenance plan for the next few years. And you are welcome to go call the governor and see if I speak for him, because I assure you that I do.”

Pollack acknowledged questions that were raised after both Governor Baker and Scott said in news conferences that they hadn’t spoken to each other since the snow began. Pollack said that was because she was speaking with both of them several times a day.

“I actually thought that I was helping Dr. Scott and her team by not needing them to be involved in all of the administrative conversations so they could focus on the extraordinarily difficult work of operating the system. And if that has created any confusion, I apologize, because that was my call.”

Then, it was time for Scott to address the board herself.

“During these unprecedented weather conditions, I want to start out by once again thanking the public and our customers for their enduring patience and understanding. We definitely share their frustration.”

Scott thanked the MBTA staff for their incredibly hard work over the last few weeks. She showed a presentation of photos of how the nearly six feet of snow has impacted the system, explaining that under the circumstances, there was nothing more that could be done. And she reiterated her statement that the problems the T is facing come as a result of a lack of sufficient funding.

What Scott did not do was give any indication that she planned to step down. But she did end her presentation with  a note of reflection.

I have never in all my life worked in a transit system that has more of a personal and intimate connection with the community that it serves, the people and the community that it serves.”

The Department of Transportation Board then gave Scott a unanimous vote of confidence.

Hours later, she submitted her letter of resignation to the chairman of that board, saying that while much more needs to be done to achieve a modern and first class transportation system, it’s been an honor to serve in that effort.

Listen to Beverly Scott's Tuesday press conference here.