It was a short silence, scarcely a minute, but there was so much in it. All the swirling, clashing, contradictory emotions of a match unlike any other that has ever been played, just hours after Typhoon Hagibis had blown through Japan, while the floodwaters were still high around the ground, the rescue work not finished, the repair work not even begun. No one was even sure exactly who, or how many, the silence was for. They were still counting the victims, and had been all day. At dawn the tally was four, then it climbed to nine. By the time they started the game it was 24, by half time it was 26, and it reached 28 soon after it was over.

Japan marks shining moment at Rugby World Cup in wake of Typhoon Hagibis Read more

You’d ask, then, whether they should have even been playing. And World Rugby had exactly that conversation early on Sunday morning. They decided they had to defer to the Japanese members of the local organising committee. Why play sport, why watch it, while there were still so many people missing, when the levees are broken and the rivers are overflowing, when, in Kawasaki, 16 miles to the east of Yokohama, almost a million people had been evacuated in the night, and in Sagamihara, 30 miles to the north, they were still counting how many had died in a mudslide that wiped out a street of houses.

For distraction, perhaps, and as a way of reclaiming some normality, as an act of defiance, even, a vital sign that we, at least, are alive and determined to enjoy what we’ve got.

The hosts were driven by their sense of pride, too, but, according to an executive who was in on the meeting, the main reason, the one the Japanese officials kept coming back to, was that they wanted to prove to the world that they could do it.

One of the reasons that the damage wasn’t worse here in Yokohama was that the stadium has been built in the middle of the flood basin that takes the overflow from the Tsurumi river. It’s built on stilts, to let the water run underneath. So the stadium is physically part of the city’s flood defences. And now it is spiritually part of them, too.

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Officials slept in the stadium on Saturday night, while the typhoon blew outside, so they could start assessing the damage the minute it stopped. At dawn the repair crews came in, and started pumping the floodwater out of the dressing room, where it was an inch deep, while the fire-service triple-checked all the electrics. Later they hosed down the pitch, to clear off the mud and debris. Meanwhile the organising committee were coordinating with the government and regional authorities, with all three emergency services, the water authorities, the road authorities, the train and bus companies, trying to untangle a cat’s cradle of complications.

In Japan all the talk has been about how this World Cup is about omotenashi, Japanese hospitality. The word doesn’t exactly translate, but, in the sketchy understanding I have of it after four weeks here, it’s about doing more than your very best to please your guest.

Facebook Twitter Pinterest Isileli Nakajima, left, celebrates with Yu Tamura after the final whistle. Photograph: Jae Hong/AP

But this was several steps further again, well beyond what anyone could have expected. Which might be why so many people got it all so wrong in the days before the match. Why they imagined that Japan wanted to have this match cancelled, that they would rather have been awarded the draw than face the Scots, a team against whom they had only ever lost. They even suggested it was all part of some grand conspiracy to hobble the Scots.

The chief executive of the Scottish Rugby Union, Mark Dodson, got it all wrong too. Dodson let fly about how the SRU had taken legal advice, raged how he wasn’t going to let his team be “collateral damage”. It was an embarrassingly wild misreading of what’s been going on here, of the mood among the Japanese, and how determined they were to play, and to win, this game.

Facebook Twitter Pinterest Fans enjoy Japan’s victory over Scotland. Photograph: Anne-Christine Poujoulat/AFP via Getty Images

That silence gave way to the Japanese national anthem, Kimigayo. They have a complicated relationship with the song in Japan. There are a lot of people who prefer not to sing it. Which is why, during this tournament, they have been running a campaign encouraging the fans to join in with it. Tens of thousands did here, a stirring, solemn rendition that seemed to swell louder and louder until it echoed all around the city. And you knew then that Scotland were done for, that they were up against a team who were being driven by powerful forces, far beyond anything they had to muster themselves, a team who, like their country, were determined to prove to everyone that they could.

In that first half Japan unleashed a 30-minute spell of rugby of such ferocity, such focus, and intent, it would have cut apart any team in the tournament, including South Africa, who they will play on Sunday. Scotland play a fast game themselves, but they were out-matched here, and utterly overwhelmed, by a team who were fitter, sharper, quicker. Scotland were in tatters after that, and it was to their credit that they fought back the way they did.

As for the Japanese fans, they all seem to believe that anything is possible now, and after what happened this Sunday evening, who would ever say otherwise.