The message from Boston transit authorities - shared early in the morning via Twitter - was clear: "Go/stay home."
As the manhunt stretched into the afternoon, Amtrak stopped all trains on the heavily traveled corridor between New York and Boston. Its service from Boston to Maine was also halted. All major intercity bus lines suspended service to the area. Authorities also stopped service on commuter trains into Boston as well as the city's subway - called the T - and the city's buses.
After an intensive search yielded no suspect, authorities lifted the stay-indoors warning Friday evening and the transit system started running again. The suspect was later discovered hiding in a boat parked in the backyard of a home in suburban Watertown, Mass.
Amtrak announced it would resume limited service Friday night and regular service would be available Saturday.
Greyhound spokesman Timothy Stokes said that the company's bus service won't resume in Boston until early Saturday morning. The first express bus service into Boston will leave New York City at 2 a.m. Saturday, he said.
Only air travel functioned normally throughout Friday. Planes took off and landed mostly on schedule at Logan International, although passengers entering the airport drew extra scrutiny from state police.
All major highways in the region remained open except in Watertown, the center of the manhunt. But they - and most city streets - remained eerily empty as people heeded the government's advice and stayed home.
"I'm just like everybody else in greater Boston, just staying at home, glued to the television," said Bob Trane, an elected alderman in Somerville, Mass., a densely populated city minutes from downtown Boston. "There is nobody out in the streets, very few cars, very few people walking."
Elsewhere, travelers scrambled to find a way home.
Stranded by the Amtrak shutdown, the Rev. Victoria Weinstein passed the time with a beer in a New York bar. She weighed her options for getting home to a Boston suburb.
"I have my Plan A, B, C, and D," she said. There were rides with friends, family or waiting a day. She even considering hitching a ride with a stranger from New England she met at the bar.
"I really just want to be home with my community," said Weinstein, a Unitarian Universalist pastor. "I'm just thinking about all the people whose hearts are broken." MegaBus, which canceled 35 trips to and from Boston Friday - affecting about 2,500 passengers - said it will also cancel its 6 a.m. and 8 a.m. trips out of Boston Saturday.
Travelers whose trains or buses were canceled are getting full refunds. All airlines allowed passengers scheduled for Friday to change flights to other days, although policies varied widely. Grace periods ranged from a few days on airlines like American and Delta, while United Airlines is giving passengers up to a year from the date they purchased their tickets to fly.
Passengers trying to leave Boston by air were met by Massachusetts State Police searching vehicles at entrances to Logan. The airport handles about 1,000 flights a day and has been operating at a heightened level of security since Monday's attack, according to Matthew Brelis, director of media relations for MassPort, the public agency that runs Logan.
Government officials refused to say why flying was the only form of mass transit allowed.
But airports are a very different environment than bus or train stations. Every person and piece of luggage moving through an airport goes through a security screening. Each passenger's name, date of birth and gender is compared to those on terrorism watch lists. And before boarding a plane out of town, each person must pass through a checkpoint where police have ample time to compare them to photos of suspects.
Friday's manhunt capped off a tiring and emotional week for Boston residents.
"This thing just doesn't stop. It's been constant for the past week," said Ian Deason, director of Boston operations for JetBlue, the largest airline in the city with about 120 daily flights.
He noted that pilots and flight attendants resting in a crew lounge prior to their flights were "glued to the TV."
While Friday's mass transit shut down was unusual it wasn't the first closure.
Boston cut off the T for two days in February. The Massachusetts Bay Transportation Authority shut down all bus and train service ahead of Hurricane Irene and Superstorm Sandy. New York also shut down its public transportation system in advance of the storms.
New York's subways shut down after the 9/11 terrorist attacks, but limited parts were quickly restored. The first subway car ran just 2 hours and 28 minutes after service was halted, although parts of the system took days to resume.
London's July 7 bombings - in which four suicide bombers detonated themselves aboard three trains and a double-decker bus in 2005 - temporarily crippled the European capital's transit system. The next day, the majority of the system reopened.
In Los Angeles, buses, freeways and the airport were shut down following the 1992 riots. Bus service resumed three days later when schools reopened and a dawn-to-dusk curfew was lifted.
Even when Boston's public transportation system starts up again, some Bostonians are likely to change their behavior.
Maria D'Amico, 23, started this week to only sit in the front or back of the subway.
"If anything happened on the train, it would probably happen in the middle," she said.
Back at the airport, passengers had to adapt with no mass transit linking them to the city center. Private cars, taxis and the Logan Express - a bus service to suburban park-and-ride facilities - were still able to enter the airport.
The biggest hassle for travelers was waiting for a taxi. Brelis described the lines as "exceedingly long" during the late morning. Officials were asking people to share cabs to nearby location. The backlog cleared by afternoon.
James Kearney, an information technology consultant from East Amwell, N.J. was in town for business and managed to make it home on a United flight at 10 a.m. He said via email that the 15-mile trip from the Marriott in the western suburb of Newton, Mass. to Logan on the Massachusetts Turnpike "was extremely quiet during rush hour."
Once at the airport, he said, the situation was "pretty standard."
"Even security was fast and uneventful," Kearney wrote.
Kacey Brister, a senior at Louisiana State University, was supposed to have an interview for a public relations job in Boston at 3 p.m. Friday. She was flying on Southwest Airlines from New Orleans to Boston via St. Louis.
Before boarding the last leg of her trip, Brister said that everyone was fairly calm at the gate.
"The biggest concern for most people was how they were going to get from Logan to their hotel, home," she wrote in an email, adding that there was "a sense of camaraderie between passengers."
Not everyone was so calm, however. "My mother has begged me" to turn around, she said.
Associated Press writers Mark Jewell in Somerville, Mass., Raphael Satter in London, Joshua Freed in Minneapolis and Bree Fowler and Anne D'Innocenzio in New York contributed.