I can't wait for the end, I bet it's gunna be epic XD
I'm guessing Conan will have some epic infiltration mission with some of his allies, and possibly even a lot of main characters dieing in the process (I have a bad feeling Haibara may die in the end, or at least get mortally wounded to some degree but magically survive).
Then later just when Gin is pointing a gun at Haibara or Ran for whatever reason a shadowed force will kick a soccer ball and knock the gun out of his hand.
Gin: "Who are you?"
Conan: "Kudo Shinichi, detective"
Gin: "WHAAAAAAAT?!?"
Yeah well that may or may not happen but it's fun to guess. The main reason why the final battle is so hard to predict is because we don't know who the boss of the BO is :???:
Also as for the fact that the organization may be huge, I think that the boss/Gin will be taken care of by Conan and friends while the FBI and people take out the small fry.
Also, as for Conan taking a gun in hand, it's possible. The only thing I'm 99% sure he won't do is try to kill anybody, even Gin despite all that guy has put him through. That being said, Gin and people still might die from the BO base self destructing. That's another one of my assumptions; near the climax the base will start to self destruct, or a massive fire will break out, cuz... doesn't that always happen?