All subway and rail service throughout the New York metropolitan area was either fully or partially running Tuesday after a full shutdown of the mass transit system ahead of Tropical Storm Irene. Many others in the region were still dealing with the aftermath of the storm, as flooding and power outages continued.

The head of the $2.8 billion fund that will be used to compensate people made sick by the September 11 attacks announced final rules governing the fund, including expanding the geographical area covered.

New York City officials are keeping a close eye on one of the steeples of a more than 100-year old church in Brooklyn, following Tropical Storm Irene.

City agencies fanned out over the city to clear trees from streets on Monday. Using data from 311 calls, parks officials estimate that around 1500 trees have fallen in the streets, with many more toppled in city parks.

PHOTOS. Tropical Storm Irene walloped much of upstate New York — including Delaware County where the torrential rains sent water gushing down the main streets of rural villages in the Catskills proved deadly and caused widespread damage in the area.

Connecticut Governor Dannel Malloy took a helicopter ride across the state get a first hand, aerial view of the damage that Tropical Storm Irene caused over the weekend. The storm that barreled up the East Coast was blamed for two death in Connecticut, flooded roads, and knocked power out to more than 700,000 homes and businesses across the state.

State Comptroller Thomas DiNapoli rejected a $27 million no-bid contract between the state education department and an education technology company owned by Rupert Murdoch's News Corp.

Ordinary homeowners insurance will cover much of the damage Tropical Storm Irene caused to homes and businesses in the tri-state area — but it won't pay for repairs to basements or foundations affected by flooding.

Two days after hurricane Irene brought New York’s mass transit to a standstill for the first time in its history, passengers at the city’s major transit hubs were scrambling in its aftermath despite partial restoration of service.

Clean-up crews in New Jersey are facing massive flooding and debris as they work to restore service to the 625,860 customers who lost electricity during Hurricane Irene.

The storm that brought the city to a standstill over the weekend with soaking rains and high winds has the potential to disorient erds of thousands of birds at the peak of their annual August migration.

New York City was largely spared from the wrath of Tropical Storm Irene, but the storm claimed lives in upstate New York and suburbs as residents around the tri-state remained awash in flood waters and hundreds of thousands were without power.

Subway service was restored for Monday and many who evacuated from flood-prone areas returned to their homes as the tri-state area began the clean-up in the aftermath of Tropical Storm Irene.

Many residents of Red Hook who chose to ignore the mandatory evacuation order and weather the storm in their low-lying Brooklyn neighborhood emerged from their homes Sunday and were not surprised by the extent of damage that Tropical Storm Irene left in its wake.

PHOTOS. From flooding to downed trees, see how Tropical Storm Irene has affected the Tri-State area. You can share your Hurricane Irene experiences or read what others were doing while we blogged the aftermath of the storm.

Officials said most subway service would be restored by 6 a.m. Monday while many who evacuated from flood-prone areas returned to their homes as the tri-state area began the clean-up in the aftermath of Tropical Storm Irene.

WNYC AM820 is off air due to flooding in New Jersey. You can continue to hear WNYC on FM93.9, at WNYC.org and at NJPublicRadio.org.

WNYC welcomes NJPR listeners.  Stream our special coverage.

Despite the order to evacuate flood prone areas, many living in public housing in low-lying Far Rockaway decided to ride out the storm — even as a police van blaring the warning "a dangerous hurricane is approaching - you are ordered to leave" circled the neighborhood on Saturday.

As the rain picked up in intensity in Morristown, New Jersey, on Saturday, Kim Tiburt 42, was using the overhang at the New Jersey train station for cover while she tried to figure out where she could get shelter from Hurricane Irene.

UPDATE: 6:56 p.m. There were nearly 121,000 customers in New York City without power after Hurricane Irene barreled down on the region Sunday morning, bringing rains that could force the utility to cut power to Lower Manhattan if flooding becomes widespread.