Andy Byford, who was brought in to help rescue New York City’s failing subway, resigned as its leader on Thursday, ending a successful but tumultuous two-year tenure marked by repeated clashes with Gov. Andrew M. Cuomo.
Mr. Byford had been widely praised by riders and transportation advocates for reversing the steep decline of the nation’s largest subway, and his departure raises significant questions about the future of an antiquated system struggling to become a 21st century transportation network.
“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,” Mr. Byford said in a statement.
His departure, which was first reported by Politico, could jeopardize the current campaign to fix the subway. He had ambitious plans to transform the system and a unique mix of charisma and a dogged work ethic that made New Yorkers believe in him. His arrival in January 2018 was celebrated as a turning point for the subway, and profiles in The New Yorker and on 60 Minutes followed.
Mayor Bill de Blasio, who has also had a difficult relationship with Mr. Cuomo, lamented Mr. Byford’s departure.
“This is a real loss for New York City’s subway and bus riders,’’ he said on Twitter. “The M.T.A. needs people like Andy Byford — now more than ever.”
When Mr. Byford took over running the subway, only 58 percent of trains were on time. There were near constant meltdowns and several train derailments raised safety concerns.
Mr. Byford helped push the on-time rate over 80 percent through a series of operational changes and a focus on the basics. He said he wanted to bring the on-time rate into the 90s and proposed an ambitious overhaul of the subway’s ancient signal equipment.
Some believed Mr. Byford’s rock star status may have irked Mr. Cuomo. They compared the dynamic to Mayor Rudolph W. Giuliani and his police commissioner, William J. Bratton, who resigned in 1996 shortly after being on the cover of Time magazine.
When Mr. Byford publicly questioned Mr. Cuomo’s decision to call off the shutdown of the L train tunnel between Manhattan and Brooklyn, Mr. Byford suddenly found himself sidelined. The two men did not speak for four months in 2019.
Their relationship appeared to improve in recent months. Then Mr. Byford tried to resign in October, citing concerns over budget cuts and interference by Mr. Cuomo’s office. His bosses at the transit agency convinced him to stay, but the détente did not last long.
“Andy Byford will be departing New York City Transit after a successful two years of service and we thank him for his work,’’ said Patrick J. Foye, the chairman of the Metropolitan Transportation Authority, the agency that operates the subway.
Mr. Foye’s statement did not hint at the problems that had been unfolding behind the scenes in recent months. He thanked Mr. Byford for improving the subway and helping to secure new funding for the system, along with Mr. Cuomo and state lawmakers.
Officials at the authority will face a big decision in replacing Mr. Byford. Sally Librera, Mr. Byford’s top lieutenant and the first woman to lead the subways division, could be a top contender. She is a respected technocrat who joined the transit agency in 2004 and has taken a prominent role in touting the subway recovery.
Mr. Byford had developed a cult following among transit enthusiasts, who plastered stickers with his face on street posts with the slogan: “Train Daddy Loves You Very Much.” He could often be found greeting riders at stations with a huge smile and focused attention on the needs of disabled New Yorkers. He even once grabbed a broom to help clean a flooded station.
When Mr. Byford’s future seemed uncertain in April, Corey Johnson, the City Council speaker posted on Twitter: “Losing Andy would be a tremendous loss. In Andy We Trust.”
On Thursday, Mr. Johnson posted a one-word reaction on Twitter: “DEVASTATED.”
Transit advocates immediately raised concerns about his departure, calling it “a terrible day for riders.”
“It’s an unfortunate and predictable outcome when you have M.T.A. leadership that work in a highly politicized environment,” said Rachael Fauss, a senior research analyst at Reinvent Albany, a watchdog group. “It’s going to be extremely difficult for the M.T.A. to bounce back from this, it’s going to be challenging to find someone capable who will work in this environment.”
Mr. Byford came to New York after leading the subway in Toronto, where he won an award for transit system of the year from the American Public Transportation Association. He has also worked on both London and Sydney’s transit networks.
The Metropolitan Transportation Authority, which oversees the subway and buses, is facing a major financial crisis that could deepen if there is a recession. Transit leaders are planning to cut hundreds of workers and they have considered service cuts.
At the same time, subway officials are planning an ambitious effort to modernize the system after Mr. Cuomo convinced state lawmakers to approve congestion pricing, a plan to toll drivers entering Manhattan to raise $15 billion for the transit system.
Mr. Byford was key to those plans and it remains to be seen whether his successor will be able to carry them out on the same aggressive timeline.
Mr. Cuomo must deliver on his many promises to fix the subway, said John Raskin, the co-founder of the Riders Alliance, a public transit advocacy group.
“The future of the transit system hangs in the balance,” Mr. Raskin said.