New Yorkers braced for a snarled commute Monday as transit officials scrambled to resuscitate the nation’s largest transit system.‬

Subway service had resumed by 6 a.m. and was largely operating with the exception of some express trains. Officials warned that trains would likely be less frequent and more crowded.

Subways were running better than the Metropolitan Transportation Authority had expected as late as Sunday night, a spokesman said

But many trains from the suburbs weren’t running—stranding hundreds of commuters who use them to get to work. Metro-North Railroad and New Jersey Transit were going to remain almost completely shut down. Between the two railroads, only a small New Jersey Transit branch to Atlantic City would run.

The Long Island Rail Road was set to run a near-normal rush hour, the Metropolitan Transportation Authority said. Some service would remain suspended in eastern Long Island.

On Sunday, workers on the region’s transit systems confronted a daunting list of problems: fallen trees and utility poles; flooded rails and train yards; power outages; broken signals; and, in one case, a giant pile of mud on the tracks. Even when all that’s fixed, trains and their crews will have to be redeployed, a process that amounts to a challenge not unlike the game of “Tetris.”‬

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