My original plan had been to combine Tokyo, Nikko, Hakone and Takayama in a 10-day trip right before returning to Germany. However, this plan didn't seem like such a good idea anymore after the earthquake and tsunami in March, and the resulting nuclear situation in Fukushima. I thought about it for a long time, but in the end, I decided to go anyway - I just couldn't imagine having lived in Japan for 6 months without ever paying a visit to Tokyo. The only modification I made was to leave out Nikko (just 150 km from Fukushima, which seemed a little close), and instead throw in a visit to Kanazawa.
My first impression of Tokyo was that everything appeared to be normal. Just like there had never been an earthquake or nuclear crisis in a power plant that is just 250km away. After a while, however, I started to notice many little things, small pieces of evidence that there was indeed an ongoing crisis. Together, all these little things created a slightly eerie atmosphere - maybe more in my mind than it was really evident by looking at the bustling Tokyo crowds - but still, eerie.
One of the most evident signs of crisis were the metro escalators. My guess is that at least two thirds of them were out of service. They were blocked with signs that I couldn't read but that probably said that energy conservation is more important than comfort right now.
Another sign was the lack of tourists. I was the only guest in a four-bed dorm room in my hostel, and there was scarcely anybody to be met in the common areas. There were invitations to fold paper cranes posted around the hostel, and signs asking to conserve energy by switching off the air conditioning. Many museums were nearly empty where I would have expected crowds. Several others were closed or only partially open, mostly without explanations in a language that I was able to read.
A final thing that contributed greatly to the eerieness I felt was the certainty that the drinking water contains radiation. I regularly checked a crowd-sourced map of public and private Geiger counter readings, and to be sure the measurements were way below the thresholds. Still, the knowledge was somewhat offputting. I was accustomed to drinking tap water and refilling my water bottle for free, but in Tokyo I ended up buying supplies of bottled water instead.
Tokyo might have been empty of tourists, but it definitely was not empty of people. The subway trains were still full at rush hour. I managed to get a seat in one during morning rush hour (just because the hostel was located close to the terminus in Asakusa), and was very nearly flattened in another during evening rush hour, so I guess my Tokyo subway experience was almost complete. Not quite, however: I didn't see employees pushing people into the train. Guess I didn't take the right subway line for that ;-)