Service on one of the subway's main services, the C line, which passes through its three most populous boroughs, was halted for up to five years after a shopping trolley containing wooden blocks was set alight on Sunday.
The fire was in an unmarked room containing 600 electrical devices that are used as power signals, melting thousands of wires and disabling the signalling on the A and C lines that link the top of the island of Manhattan to the edge of Queens via Brooklyn. Repairs will cost millions and, in the case of the C line, will take many years.
Between them, the two lines carry 580,000 passengers each weekday. The damage was inflicted at one of the most sensitive points, leaving commuters stranded.
"It's major, major damage," said the Transit Authority president, Larry Reuter. "It's a barbecue. It's black and melted."