MONTPELIER, Vt. (AP) — 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 big city commuters had to make do with slowly reawakening transit systems.

The storm left millions without power across much of the Eastern Seaboard, killed at least two dozen 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 caused the worst flooding in a century in Vermont.

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. Gov. Peter Shumlin called it the worst flooding in a century, and the state was declared a federal disaster area.

“We prepared for the worst and we got the worst in central and southern Vermont,” Shumlin said Monday. “We have extraordinary infrastructure damage,” including communities that were cut off, hundreds of roads closures and the loss of at least three historic covered bridges.

Video posted on Facebook showed a 141-year-old covered bridge in Rockingham, Vt., swept away by the roiling, muddy Williams River. In another video, an empty car somersaulted down a river in Bennington.

“It’s pretty fierce. I’ve never seen anything like it,” said Michelle Guevin, who spoke from a Brattleboro restaurant after leaving her home in nearby Newfane. She said the fast-moving Rock River was washing out the road to her house.

Officials at one point thought they might have to flood the state capital, Montpelier, to relieve pressure on a dam. But by Monday morning that threat had abated.

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.

Only about 50,000 power customers in New York City went dark, but people there had something else to worry about: getting to work Monday.

The metropolitan area’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 partially restored at 6 a.m. Monday.

Commuter rail service to Long Island and New Jersey was being partially restored, but the Metro-North Railroad to Westchester County and Connecticut was suspended because of flooding and mudslides.