Calm was restored by 9 p.m. Monday after a line of thunderstorms moved through Long Island, disrupting morning and evening rush-hour commutes as well as power to more than 25,000 customers.

Several trains had been canceled and others combined after the storms caused signal problems during both rush hours, the Long Island Rail Road said.

On top of signal disruptions, Amtrak discovered a problem in one of the East River tunnels, leading to the first wave of service cancellations during the afternoon rush hour, LIRR said.

At 9 p.m., the New York City airports still reported delays as planes were rerouted around storm clouds. Flights were arriving at Kennedy and LaGuardia airports up to about 2 hours and 15 minutes late, down from three hours in the afternoon, according to the FAA's website. Departures at Kennedy faced delays of up to 90 minutes, while it was up to 30 minutes at LaGuardia, the FAA said.

But elswhere, calm was largely restored by 9 p.m.. Outages had been fixed for all but about 1,000 customers, the Long Island Power Authority. Train service was back on schedule, the LIRR said.

The National Weather Service in Upton lifted the storm warning and flood advisory by 7 p.m., forecasting mostly clear skies at night.

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Isolated thunderstorms and scattered showers may return Tuesday afternoon, the Upton service said.

Tuesday's flash storms had made a mess of the morning rush-hour commute, flooding roads, delaying trains and airplanes, and at one point knocking out power to more than 25,000 LIPA customers.

The Long Island MacArthur Airport in Ronkonkoma got the biggest drenching on Long Island, accumulating more than four inches Monday, according to data from the National Weather Service. Quarter-sized hail was reported in Central Islip and Ronkonkoma, the service said.

The morning storms were "really heavy rain makers" that moved through "the whole Island," meteorologist Brian Ciemnecki said.

The morning storms caused signal problems that prompted the suspension of service on the Babylon and Port Jefferson branches Monday morning and also caused scattered westbound delays systemwide of up to 20 minutes, officials said. Service was restored at 11 a.m.

"Weather permitting, we are expecting a normal p.m. peak," spokesman Sal Arena had said.

It turned out the weather did not permit: The LIRR wound up canceling at least nine afternoon rush-hour trains bound for Long Island due to the weather and problems in one of Amtrak's East River tunnels.

There were minimal delays at Long Island MacArthur Airport, according to its website.

At the peak, LIPA reported 25,068 outages Monday morning, most of them in Suffolk -- most of those in the Town of Brookhaven.

LIPA spokesman Mark Gross said emergency crews had been diverted from Nassau County, where storm damage was minimal, to Suffolk.

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Gross said the bulk of the damage was from lightning and gusting winds, which he said knocked down trees and tree limbs -- and power lines.

He said emergency crews would work "extended shifts" to get customers back online.

"They're out there in full force," Gross said, noting there were almost 200 separate damage sites that needed to be addressed by those crews. "They're assessing damage and they'll be out there all day into night to get the job done."