A Tokyo resident on facing his fear and living with earthquakes

Everyone who lives in Tokyo mentally rehearses where they will be if the Big One strikes. When I first arrived as a student, I found myself walking through a sprawling, crowded, low-ceilinged shopping centre underneath the city's business district, pondering the apocalypse.

The word didn't seem inappropriate. Tokyo has a remarkable history of almost biblical destruction. In 1923, a 7.9-magnitude earthquake and tsunami levelled much of Yokohama and Tokyo, crushing, incinerating or drowning at least 100,000 people. Even the national icon, Mount Fuji, looms threateningly 60 miles away, ready to spew millions of tons of ash down on the world's largest metropolis.

I've often been asked: how do people with millennia of horrific collective memories manage to repress them and get on with life? One answer is that they don't. The fear of earthquakes, tsunamis and volcanoes runs very deep among most Japanese. Time and again after 11 March 2011, we would hear stories of people diving for cover, fleeing their houses or running from the coast the moment the tremors began – instincts that would often save their lives. But thousands of others ignored those ancient responses in the disaster that left nearly 19,000 dead or missing, and a huge swathe of the Fukushima countryside contaminated with radiation from the triple meltdown at the Daiichi nuclear plant.

In Ofunato, a city with a history of devastating tsunamis, Akio Komukai, a factory worker, described speeding away from the coast after the quake struck and meeting children on their way home from school. "They were walking towards the sea and I rolled down the window of my car and shouted: 'There's a tsunami coming, you need to run away!'" The young people looked at the 61-year-old, said "Okay, okay," and kept walking – an episode one imagines being repeated in its way down through the centuries. "We forget that the sea is close because we build next to it," Akio said. "Then the tsunami comes and washes away the houses and you can see the sea again. And we're reminded."

Urbanites can believe that they are safe from natural disaster. They are safer than ever before, after all. But periodically they are given a reminder that the cost of the collision between primordial seismic instability and life in our most sophisticated cities can still be terribly high. The 1995 Kobe earthquake took 6,400 lives, injured 400,000, wiped out 2.5 per cent of the nation's GDP and orphaned dozens of children. What would happen if it was Tokyo, many wondered.

On 11 March 2011, I was standing with my partner, Nanako, in Shinagawa Station, one of Tokyo's biggest train hubs. It was a crisp, sunny afternoon during one of the more pleasant times of the year in the city, and it was a happy time for us. We were waiting for the birth of our son, Luka.

The quake began, not like many quakes do, with a jolt, but with an almost lazy undulating rocking motion that slowly built in intensity until the station's roof rattled violently and glass fell on to the platform. A woman somewhere screamed, others clung to husbands, wives or children. A man ran for the exit and fell over the ticket barrier. It is rare to see Tokyoites panic, and it terrified me. We stood frozen to the spot, hearts thumping violently and watching the roof, silently praying it wouldn't fall on our heads. The tremors seemed to go on forever. Kobe lasted for 20 seconds; later we would hear that the shaking from what became the 2011 Tohoku earthquake and tsunami went on for nearly six minutes.

The explosive force that we felt at 2:46pm had been released by one of Japan's most unstable faults, about 19 miles beneath the sea off the northeast coast. The earth's crust is made up of eight large tectonic plates that have been moving and grinding against each other for millions of years, and the largest – the Pacific plate – dips under the slab of rock beneath Japan's main island, Honshu. Eventually, the stress of that friction is released, but seldom as violently as on 11 March last year. Scientists would later estimate its force at more than one million kilotons of TNT – the atomic bomb dropped on Hiroshima in 1945 released 15 kilotons.

The following morning, I set off for the devastated northeast coast with two colleagues to report for The Independent. As we sped along the highways, deserted apart from ambulances and army trucks, we listened to radio bulletins about what would become the biggest story of all – a fire at a six-reactor nuclear plant in Fukushima. The announcer's adjective-free, rigidly factual coverage, filtered through the emotionless tones of a professional translator, gave little sense of the urgency, but the news was terrifying nevertheless. A reactor core in the Fukushima Daiichi nuclear plant may have melted, the announcer informed us. An explosion had torn the roof from the number one reactor building. Radiation had leaked into the atmosphere. Evacuation orders were issued to 20,000 people living within 10km (6.2 miles) of the plant. At tea time the Prime Minister, Naoto Kan, announced to millions of Japanese that the safety perimeter has been extended to 20km. And we were driving towards it.

Throughout the following days of reporting, the news filtered in through our mobile phones. Foreigners were fleeing the capital amid fears of nuclear contamination. On 17 March, the British Embassy, until then a steady, sober voice in the storm, advised its citizens to "consider leaving Tokyo and the area north of the capital." The US Embassy, meanwhile, was secretly planning the evacuation of 90,000 of its citizens. The US Seventh Fleet has moved its ships, aircraft and personnel to open sea, away from Tokyo, because its equipment detected high levels of radiation.

Among Nanako's texts, one that said the stores had run out of milk and water. "I had nightmares and woke up… I'm thinking about you every second," she wrote. "U have to come home asap!! Please!!!!! My tears will not stop … xxx."

That was the final straw. The next morning, I hitched back to Tokyo with a crew of emergency workers. The normally bustling capital felt like the blood has been drained from its veins. Rolling power cuts, food and petrol rationing, the growing death toll and the constant threat of more aftershocks and tsunamis filled TV screens. Self-Defence Force troops were shown dropping water from tungsten-reinforced planes flown 300 feet above the Daiichi plant's overheating reactors.

Thousands of schools were closed and factories and businesses were operating reduced hours to save electricity. Many foreign friends in the city had already quietly left, drifting off to Osaka, Hong Kong, South Korea or Thailand.

But even as panic flickered on the edges of Tokyo life, all around me I could see salarymen going to work in the mornings, housewives queuing for water or milk after dawn. Throughout the worst week of the crisis, a diligent clerk at my local video store phoned daily to remind me that I had failed to return a DVD.

In the days, weeks and months ahead, there would be comfort in that thought. Luka was born in June. His mother had been briefly a nuclear refugee, fleeing Tokyo for Osaka when he was still inside her belly. He appears mercifully unharmed by that ordeal. Already the extraordinary events that occurred before he was born are fading from view. Someday, perhaps, he will watch them in grainy footage and we will try to tell him what it felt like to glimpse into the abyss.

Strong in the Rain – Surviving Japan's Earthquake, Tsunami and Fukushima Nuclear Disaster, by Lucy Birmingham and David McNeill, published by Palgrave MacMillan, is available from 30 November.