Since Hurricane Irene, the M.T.A. has had an employee act as a “scribe” — officially, the Information Liaison Officer — for the duration of extreme events, like hurricanes and snowstorms. The scribe keeps what’s called an “incident chronology,” a disaster-response timeline, for the sake of institutional memory and in case there are lawsuits or the City Council complains and the authority needs to justify its actions.

The scribe sits in the situation room, overlooking the R.C.C. For both Irene and Sandy, Dan Mazzella, a native New Yorker who normally works in train scheduling, filled the role of scribe. In the hour or two before Sandy hit, Mazzella was not busy. He likens that period to a break in a symphony’s performance. “The conductor’s up like this,” he says, raising a hand, “and you have absolutely no control over when the baton drops, but you know that like a bat out of hell it’s going to happen.”

Then, inside the control center, the TV told them the surge had arrived. “All of a sudden the phones start lighting up, and you don’t have enough hands, you don’t have enough ears,” Mazzella says. “It’s nuts, the 6-Wire” — the internal communications line, which connects to the Police and Fire Departments — “starts going off, and you’re hearing that there are explosions down at the Con Ed plant, that there’s water cascading into the system here. . . .” The boards began to come back to life, the sensors in the tunnels registering the water as moving trains. New York City Transit had estimated that flooding would close a few of the 14 tunnels that go under the city’s waterways (called “tubes”), but at this time it looked as if nine of them would be lost.

‘REALITY SET IN THAT THIS IS BAD’

Among the many places where the Hudson and the East and even the Harlem Rivers breached the New York City subway system when Sandy finally hit, the recently completed South Ferry station was high on the list of the most overwhelmed. At around 10 o’clock that Monday night, just after the first of Sandy’s two major surges — one came from the south, from New York Harbor; the second came from the north a few hours later, from Long Island Sound — a National Guard truck dropped off Joseph Leader at the bottom of Broadway, so he could wade past Battery Park to check out the South Ferry station.

He already knew things were worse than anyone expected. During Hurricane Irene, in August 2011, flooding at Battery Park was bad — but not three-feet-of-water-over-Lower Manhattan bad. The area was a lake, the subway stairs at the South Ferry entrance a small cascade. As Leader was imagining all-new worst cases in his head, another engineer shouted at him. “He said to me, ‘I just got a call from Con Ed, and there’s like a 26-foot surge or wave that’s coming into the bay that they got alerted of, and they are shutting down the 14th Street plant.’ And before we could absorb that, we could see power shutting down in the city. So that was a moment when you started to say, ‘Oh [expletive].’ ”

Leader went south, toward the Staten Island Ferry landing, where he saw the first unexpected worst-case scenario: the plywood-and-plastic-sheeting barricade at the mouth of the South Ferry entrance had been trashed by timber washed in from the harbor. Then he waded back north, to the station’s other entrance, to look in on a spot where there wasn’t supposed to be flooding, even in hurricanes. But as soon as he started down the stairs at this entrance, the beam from his flashlight hit water. “Where is the water going?” he wondered. Even someone who had worked for the system since 1986, who can rattle off the names of pump stations with ease — the Mud River pump room at 60th Street, for example — was confused by what he saw.

Slowly, Leader came to understand that the water was not just coming into the station from the harbor — it was also leaving the station, heading north on the tracks, as if taking the No. 1 line uptown. Worse, it was about to enter into the Lexington Avenue subway line’s tunnel through an underground track connection invisible to riders. The M.T.A. was facing an underground assault after having mostly built its fortifications aboveground, at station entrances and vents. The other thing Leader realized as he watched the water climb the stairs in front of him was that he had to get out of there, fast.