Like Raistlin said, the purpose and instinct of the Weapons, once unleashed, is to kill of prettymuch everything on the Planet in order to give it a chance to start over again. So, just because there were no scenes specifically devoted to showing Ultimate attacking anything besides Mideel, you can rest assured that it was keeping itself occupied tearing up the countryside and such. Sapphire and Diamond just had more sense to go after targets especially dangerous to the Planet's welfare.

Ruby and Emerald just flounder around because they were only added to the game so that it could have some mega-tough optional bosses. They were never meant to be thought of specifically in regards to the plot. But, if you really wanted to do that, you could easily reason that they're just even more senseless than Ultimate.