Or maybe this current plot is intended to happen the way the author wants because in every case segments, not all characters are "present altogether" because that will convulate the story. However, it would make sense if they did that behind the scenes since we know Conan is not just a little detective, he's more than "that". Maybe he did come up with some countermeasures with someone he trusted and confided in the plans if ever there's a incoming, prevailing threat which is still looming around while delivering his deceptive performance.