Typhoon Faxai, which made landfall early Monday morning in the coastal city of Chiba, brought heavy rain and winds of 120 miles per hour, according to the Japan Meteorological Agency (JMA).
The storm then moved over Tokyo and paralyzed transport. More than 100 flights to and from airports in the Tokyo area were canceled on Monday, including 49 Japan Airlines flights and 41 by All Nippon Airways, according to the airport website. The entire Keikyu rail line, which connects Tokyo and Yokohama to Haneda Airport, was suspended.
More than 13,300 passengers were stranded at Narita International Airport overnight, according to an airport spokesperson. With highways blocked and two railways to the city center shut down, arriving passengers had no way to leave the airport.
The airport handed out 18,000 sets of water, blankets and crackers for the passengers who had to spend the night. The railways and highways slowly cleared resumed operation on Tuesday morning, allowing travelers to start trickling out into the city.
Narita is one of two international airports in the Tokyo area.
It wasn't just the area around the airport -- major subway stations in Tokyo were crammed full of commuters on Monday, all stuck waiting for bullet trains and subway services that had shut down.
The train services gradually resumed mid-morning, but all lines were delayed.
Photos show flooded streets, littered with downed trees and branches. Workers on Monday tended to signposts and lamps that had blown over, and employees at the Higashi Chiba train station inspected the roof, which was twisted and torn apart.
There has been at least one death related to the storm so far -- Tokyo police said a woman was hospitalized and died on Monday.
Ahead of the typhoon, JMA issued storm surge, flood, and landslide warnings, and asked the public to avoid going outdoors.
Junko Ogura and Sol Han contributed reporting.