New York City Transit President Andy Byford has resigned from the MTA — and this time, "Train Daddy" appears to be gone for good.

Byford, who was widely credited with turning around the ailing transit system, confirmed his departure on Thursday, after two years on the job.

“I’m very proud of what we have achieved as a team over the past two years and I believe New York City Transit is well-placed to continue its forward progress now that the MTA has a record breaking $51.5 billion Capital Program in place," he said in a short press release circulated by the transit agency.

The bombshell news broke amid an MTA board meeting on Thursday afternoon, with members of Byford's staff apparently learning of his departure for the first time. "It's unbelievable," said MTA head of buses Craig Ciprano. "This changes everything."

Throughout his tenure, Byford was said to be frequently frustrated by Governor Andrew Cuomo's decision-making, particularly as it related to the type of technology that should be used in a major subway re-signaling effort. The issue reportedly drove him to quit this past October, before later rescinding the resignation letter.

Byford was also rumored to be on the verge of leaving months earlier, in part due to the governor's sudden interference in the L train project. “Andy's a nice guy. Internally, people seem to like him,” one MTA source wrote to Gothamist. “But I'm ‘feeling’ Cuomo is acting with Transit like Trump is acting [with the] US government. Very bull-in-china-shop. But the china is heavy.”

Byford denied those rumors at the time. “I am not going anywhere—not this week, not this month, not this year, etc," he said. "We are making great strides fixing our system, and I’ll be here until that job is complete.”

(It’s worth noting that the last chairman of the MTA, Joe Lhota, denied reports that he was on his way out, only to exit a month later.)

Calls to Byford's cell phone went straight to voicemail on Thursday. A spokesperson for Governor Andrew Cuomo did not respond to Gothamist's inquiries.

In a statement, MTA CEO Pat Foye thanked Byford for his service. "Andy was instrumental in moving the system forward, enacting the successful Subway Action Plan and securing record capital funding with the Governor and the Legislature, and we wish him well in his next chapter,” he said.

On Twitter, City Council Speaker Corey Johnson summed up the feelings of many officials and straphangers who valued Byford's commitment to turning the MTA around: "DEVASTATED."

UPDATE 2:00 p.m.: Cuomo addressed the surprise resignation during an unrelated press conference on Thursday. "I think Andy Byford is a good man. I think he’s done a lot of good over his two years," Cuomo said. "Fundamentally the way the MTA operates is they have a very strong team, and they’ve gotten stronger. But he’s a good man and I wish him well."

Pressed on whether his own fractured relationship with the NYC Transit president might have pushed him out, Cuomo replied, "I don’t think there’s any truth to the fact that he couldn’t get along with me. I’ve had a fine relationship with Andy."

Several advocates, meanwhile, have pinned the blame for Byford's resignation directly on the governor's actions. In a statement, the good government group Reinvent Albany noted, "Byford is widely known to have chafed at the politicization of the MTA under Governor Cuomo, whose penchant for secretiveness, message control and top-down directives conflicted with Byford's philosophy of building trust through consultation, personal accountability and transparency."

Elsewhere, Speaker Johnson, apparently still in the denial stage, is trying to get a hashtag (#BringAndyBack) trending to convince Byford to reconsider. In response, a Cuomo-appointed spokesperson, Sarah Feinberg, pushed back against the idea that his departure is indicative of a crisis within the agency.

"With all due respect to Andy—I enjoyed working with him—but [NYC Transit] is not about one person, it’s about the more than 50k men and women who keep the system running and the millions who ride," she wrote.

This is a developing story — we'll update as more information becomes available. Additional reporting by Stephen Nessen.