Limited service started Thursday morning with long lines of people waiting for packed buses.
The MTA will restore limited subway lines after Hurricane Sandy and will suspend fares through Friday.
The authority is considering getting some trains at dry stations moving Wednesday.
Mayor Bloomberg said subway service will be shut down for the rest of the week after Hurricane Sandy.
Chairman Joseph Lhota said the MTA has never "faced a disaster as devastating" as the one left by Sandy.
Most of the FDR Drive was also closed Monday because of the storm.
Low-lying areas including Red Hook, Battery Park, and Far Rockaway, were flooded Monday.
The MTA's East Side Access project is expected to be completed in 2019.
James Neverson, 63, was on his way to work when the car hit him Tuesday, officials said.
The MTA is still investigating why the blast rained debris on Second Avenue and 72nd Street.
Firefighters rushed to Second Avenue and E. 72nd Street after a big blast shook the area on Tuesday.
Thieves are not only grabbing iPhones. Eighteen MTA facilities have been ripped off this year.
A person was in cardiac arrest after being hit by a 1 train at Columbus Circle, officials said.
The MTA plans to restore cuts to the M9's route, Assembly Speaker Sheldon Silver said.
The M101 will see more midday service, while the M102 and M103 will see less under an MTA proposal.
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