New York City’s former subway chief, Andy Byford, won’t be returning to New York after all. Instead he is going back to the European city where his transit career began.

On Wednesday, the mayor of London, Sadiq Khan, confirmed Byford’s appointment as commissioner for Transport for London, the agency that runs that city’s sprawling subway and bus system

“I am delighted to be taking up the role of Commissioner and to have been chosen to lead the organization where I started my transport career over 30 years ago,” Byford said.

Major transit agencies in London, New York and elsewhere around the world have seen their ridership and revenues plunge as the coronavirus pandemic prompted stay-at-home orders and people avoided trains and buses.

Now, as the pandemic eases its grip in many places, transit agencies face the challenge of regaining the confidence of riders and finding ways to protect the public’s health.

Byford, one of the most revered transit leaders in recent New York history, left the Metropolitan Transportation Authority in January, after clashing repeatedly with Gov. Andrew Cuomo.

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Critics across the political spectrum faulted the governor for failing to embrace the man he had hired to run the foundering system. But Cuomo’s allies said Byford did not do enough to find a way to get along with the governor, who controls the system.

In Byford’s resignation letter, he suggested that the governor had sidelined him by initiating an agency overhaul that took away some of his power.

The governor would also hold meetings about the subway system and not include Byford.

At the time of his resignation, Byford said he would like to remain in New York, a city he had grown to love.

When Cuomo, a Democrat, tapped Byford to run the country’s largest subway and bus system in 2017, it was embroiled in its worst crisis in decades. Years of mismanagement and neglect had caused service to crater.

Only 58% of trains were arriving on time, the worst performance since the 1970s, and a handful of derailments left riders worried about their safety. The system became chronically unreliable, upending the routines of people who counted on the subway to get them to work.

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The situation got so bad that Cuomo declared the subway to be in a state of emergency.

During Byford’s tenure, he helped implement an $836 million spending plan to stabilize the system, which included upgrading tracks, focusing on basic maintenances and plugging leaks that led to flooded train tracks.

He and Cuomo also lobbied the state legislature to approve what was poised to be the nation’s first congestion pricing scheme, which would charge drivers a fee to enter Manhattan’s busiest corridors and was scheduled to start in January.

The revenues from congestion pricing were supposed to help fund a sweeping $50 billion spending plan that Byford helped draft that was meant to turn the subway into a 21st-century network with a modern signaling system.

But the plan’s prospects now look uncertain given how the pandemic has decimated the agency’s revenues and transit officials have suggested that the implementation of congestion pricing will be pushed back.

“Andy Byford did wonders for New York and put us on a track that will serve us well for a generation,” said Danny Pearlstein, the policy and communications director for Riders Alliance, an advocacy group. “London is very lucky to have him.”

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Byford is scheduled to start his new post June 29.

In London, Byford will oversee a network that rivals New York’s. The subway system and London’s Tube have similar levels of ridership; before the pandemic, both handled about 5 million riders a day.

Byford will manage 675 bus routes, twice New York City’s 327 routes.

He will also have a much more expansive portfolio than in New York, where he oversaw the subway and buses. In London, he will oversee trams, parts of the commuter rail network, 100 miles of protected bike lanes, piers on the Thames River, ferry services, a cable car and the city’s dominant bike share system. He will also share responsibility for London’s road network.

Among one of the biggest challenges awaiting Byford is the over-budget and behind-schedule Crossrail, a $22-billion train line that is regarded as Europe’s biggest infrastructure project.

He will also contend with a markedly different governance structure. In New York, Byford ultimately reported to the governor, by way of the MTA board and the agency’s chief executive. In London, he will report to the mayor.

The city’s subway system is in some ways better than New York — many of its signals have been modernized, allowing it to run trains more frequently.

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Still, Byford will have his work cut out for him, according to Christian Wolmar, a London-based transportation writer.

“God, out of the frying pan into the fire,” Wolmar said.

The politics are treacherous and the finances are bleak, he added.

Byford will report to Khan, but since the system is facing financial headwinds, Khan will have to rely to some extent on Boris Johnson, the prime minister.

Khan, a Labour Party politician, does not get along well with Johnson, his Conservative Party predecessor.

The system is “deserted and has this huge financial hole,” Wolmar said. Referring to Byford, he added, “He’s going to have to immediately go cap in hand to government and say, ‘Bail us out.’”