I'm not sure what your question is? Your subject line says Korea and Japan working together(?) and yet you reference a news blurb from 12/09 that talks about the increase in joint military exercises between Japan Self Defense and South Korean forces and the hope for future mutual cooperation.
This isn't unusual as Japan and South Korean forces have been cooperating often in recent years and have pledged for more closer relations:
South Korea, Japan to hold joint naval exercise | World Military Forum - Latest Military News | Army, Navy, Air Force, Missiles
Japan, S. Korea Discussing Closer Security Ties - Defense News
I think Japan has a problem with the North Korean government and has worked with the US. China and South Korea to try and deal with their increased military "saber rattling" and frequent missile tests.