transportation in Tokyo. what should i do?

Will come to Tokyo around this Sept, stay a week, and what is really important that i should have there? Will arrive around 11pm and its the transportation (train) still working? Until what time?

Most trains work till just past midnight. But still, there is not much to do in that few hour(s).

It depends where your hotel is. If you are not leaving the airport, Narita town is quaint and peaceful. Haneda town is modern residential area that is interesting in its own right.

The most do of Tokyo:
For the usual Traveler
Skytree and Sensoji and Shinjuku to Harajuku walk

For the extreme travveler
Wake at 0330 take a cab to Tsukiji, watch fish being auctioned at prices that could buy a house
Eat super fresh sashimi

For the Otaku
Gundam statue at Odaiba
Anime stuff at Akihabara

For the zen
Meiji Jingu and Shinjuku koen

For the Family\
Shinjuku Koen, Shinjuku zoo, Ueno shopping district

ok I misread your Question

From Tokyo you can go to Chiba prefecture. Disneyland and Disneysea

You could go to Atami
Onsen and Fuji mountain

You could go to Nikko
A Kyoto away from Kansai

There are many other options available, it really depends on what you like to see and do, or even eat.

Tokyo itself is interesting. But I wouldn't spend 2 nights in a row there. What do you like?

Will come to Tokyo around this Sept, stay a week, and what is really important that i should have there?

I'd start with this page:

http://www.japan-guide.com/e/e3051.html

Will arrive around 11pm and its the transportation (train) still working? Until what time?

Depends on what airport you are coming into, but if you arrive at 11 then you're generally should stay around the airport. Narita has several hotels in the area. Haneda on the other hand is fairly isolated and only has a few accommodation options.