(above bills are provided by my friends)
2000 yen note is first issued in 2000 to commemorate the year 2000 and Okinawa Summit (26th G8 Summit). It was planned by Keizo Obuchi and completed by then Prime Minister Yoshiro Mori.
The bill is known to have 5 of the advanced technologies to prevent counterfeiter.
It depicts Shureimon, one of the symbols of Okinawa to emphasize the importance of Okinawa for Japanese politics.
Prime Minster Mori was expecting this bill to spread out in the whole Japan but unfortunately his vision never came true.
One of reasons involves most of the ATMs and vending machines do not accept the 2000 yen bills and therefore people have few chances to receive them.
Also, there is a theory that because of the cultural factor, which in Japan emphasize the importance of odd numbers (on the contrary to western societies in general where they often use even numbers as in $20, 20 ponds, etc)
The only place this bill is widely used is Okinawa, where the local government did the campaign to spread out 2000 yens.
There is also an interesting rumor about the bill that it is created to decimate the political message from Japanese government to China, where they claim the right to own the island of Okinawa.
It therefore has an image of Shureimon to emphasize the Japanese ownership of Okinawa against China.
I don't know how much that is true but 2011 news report says LDP tried new campaign to encourage the use of 2000 yen in Okinawa to appeal LDP's emphasis and care for the Okinawa region.
At least it sounds like true that bills reflect the nation's politics very often.