The bad weather was initially expected to come mid-afternoon but came late at night instead.

The south side of Tokyo was absolutely inundated last Thursday afternoon, with half of the Tokyu lines out of service for several hours because stations south of Meguro and Gotanda had completely flooded. A lot of buildings in low-lying areas like Jiyugaoka were also flooded. HND was also temporarily shut down and a lightning strike was powerful enough to tear the asphalt in one of the runways. I think they were expecting a similar situation yesterday and decided to warn people in advance.