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The utility company said the faulty system was at its West 65th Street substation.
"That system detects electrical faults and directs circuit breakers to isolate and de-energize those faults. The relay protection system is designed with redundancies to provide high levels of reliability," Con Edison said in a statement on Monday. "In this case, primary and backup relay systems did not isolate a faulted 13,000-volt distribution cable at West 64th Street and West End Avenue."
The failure of the substation's relay systems then led to a "fault at the West 49th Street transmission substation," which triggered the power outages.
About 72,000 customers lost service during the hours-long blackout that started at 6:47 p.m. Saturday, the utility company said. They said most customers had their power restored within three hours, and all customers had electricity back in five hours.
Officials definitively ruled out either cyber- or physical acts of terrorism of any kind.
Con Ed President Tim Cawley said Sunday the system was prepared to deal with high demand, like that expected this coming week as temperatures rise.
And in Monday's statement, the company said their investigation determined the outage was not caused by transmission equipment.
Thousands of people crowded the streets Saturday evening, using their cellphones as flashlights while they tried to stay cool amid the humid July evening, where temperatures hit the low 80s.
In the theater district, marquees darkened just before evening performances were set to begin. Most Broadway musicals and plays canceled their Saturday evening shows, though some cast members staged impromptu performances in the street.
U.S. Sen. Charles Schumer said Sunday the Department of Energy's Office of Electricity should investigate the work being done by Con Edison to maintain and upgrade the city's power grid.
He added that "this type of massive blackout is entirely preventable with the right investments in our grid," encouraging a thorough investigation that could shed light on wider electricity issues that could have national impact.
New York Gov. Andrew Cuomo and New York City Mayor Bill de Blasio both said they would be directing agencies under their control to look into what happened.
The questions raised by the blackout weren't just about the power, they were political as well as de Blasio was criticized for being on the presidential campaign trail when the outage happened.
He returned to the city on Sunday, and insisted that the situation had been well-managed, that he had been in touch with his staff and started his trip back as soon as it became clear the blackout would not be quickly resolved.
"You have to take charge wherever you are, and I did that," he said.
The outage stymied subway service throughout the city, affecting nearly every line. New York City's Emergency Management Department said the A, C, D, E, F, M, 1, 2, 3, 4, 5, 6 and 7 trains had resumed running in both directions by around 2 a.m. Sunday.
No injuries were reported.
The police and fire departments brought personnel and equipment in from other parts of the city to help, including 400 police officers and 100 traffic agents, as well as 93 additional ambulances.
The outage came on the anniversary of the 1977 New York City outage that left most of the city without power.
The Associated Press contributed to this report.