Alright...

So, I ran around the Tokyo station popping baddies and rescuing hostages. I finally find two good guys. Some cat named Adam and another guy whose name I don't remember. But they won't talk to me. So I run around some more and find a few more bad guys and kill them. I go back, but the good guys still won't talk to me. Finally I get fed up and hack them to pieces, then Tomoko shows up and hauls me away in a hijacked train. I don't get it. Is this a bug, or did I miss something?

Unfortunately that's been a perpetual bug. I thought I had it fixed in the last patched but it keeps sneaking by :|

Best you can do is revert to a save just prior to Tokyo Station, if you've got one. Then give this patch a whirl. It worked for me when I tested it, but you know how things are around these parts :T

http://www.edgefiles.com/files/14526.html