NEW YORK — The storm that had been Hurricane Irene crossed into Canada overnight but wasn't yet through with the U.S., where flood waters threatened Vermont towns and New Yorkers feared a commuting nightmare as their transit system, shut down ahead of the storm, was slowly restored. The storm left millions without power across much of the Eastern Seaboard, left more than 20 dead and forced airlines to cancel about 9,000 flights. It never became the big-city nightmare forecasters and public officials had warned about, but it still had the ability to surprise. Many of the worst effects arose from rains that fell inland, not the highly anticipated storm surge along the coasts. Residents of Pennsylvania and New Jersey nervously watched waters rise as hours' worth of rain funneled into rivers and creeks. Normally narrow ribbons of water turned into raging torrents in Vermont and upstate New York late Sunday, tumbling with tree limbs, cars and parts of bridges. "This is not over," President Barack Obama said from the Rose Garden. Hundreds of Vermonters were told to leave their homes after Irene dumped several inches of rain on the landlocked state. Video posted on Facebook showed a 141-year-old covered bridge in Rockingham swept away by the roiling, muddy Williams River. In another video, an empty car somersaulted down a river in Bennington. Green Mountain Power warned that Montpelier, the capital, could be flooded twice: once in the initial storm and again if the utility decides it must release water to save the earthen Marshfield Dam, about 20 miles (30 kilometers) up the Winooski River to the northeast. "We don't want to do it. But if the dam were to be compromised, it would be a far greater effect," utility spokeswoman Dorothy Schnure said. Residents of 350 households were asked to leave as a precaution. Nearly 5 million homes and businesses lost power at some point during the storm. Lights started to come back on for many on Sunday, though it was expected to take days for electricity to be fully restored. New York's transit system, shut down because of weather for the first time in its history, was taking many hours to get back on line. Limited bus service began Sunday and New York subway service was to be partially restored at 6 a.m. Monday, but riders were warned to expect long lines and long waits. Airports in New York and around the Northeast were reopening to a backlog of hundreds of thousands of passengers whose flights were canceled over the weekend. The New York Stock Exchange said it would be open for business on Monday, and the Sept. 11 memorial at the World Trade Center site didn't lose a single tree. Mayor Michael Bloomberg defended his decision to order 370,000 residents to evacuate their homes in low-lying areas, saying it was impossible to know just how powerful the storm would be. "We were just unwilling to risk the life of a single New Yorker," he said. Irene had at one time been a major hurricane, with winds higher than 110 mph (177 kph) as it headed toward the U.S. It was a tropical storm with 65 mph (105 kph) winds by the time it hit New York. It lost the characteristics of a tropical storm and had slowed to 50 mph (80 kph) by the time it reached Canada. Chris Fogarty, director of the Canadian Hurricane Centre, warned of flooding and wind damage in eastern Canada and said the heaviest rainfall was expected in Quebec, where about 250,000 homes were without power. At least 21 people died in the U.S., most of them when trees crashed through roofs or onto cars. In an early estimate, consulting firm Kinetic Analysis Corp. figured total losses from the storm at $7 billion, with insured losses of $2 billion to $3 billion. Irene was the first hurricane to make landfall in the continental United States since 2008, and came almost six years to the day after Katrina ravaged New Orleans on Aug. 29, 2005. ___ Gram reported from Montpelier. Contributing to this report were Associated Press writers Beth Fouhy, Samantha Bomkamp, Verena Dobnik, Jonathan Fahey, Tom Hays, Colleen Long and Larry Neumeister in New York; Brock Vergakis in Virginia Beach, Virginia; Marc Levy in Chester, Pennsylvania, and Jeff McMillan in Philadelphia; and Seth Borenstein and Christopher S. Rugaber in Washington.