Well, there is so much in this episode which doesn't make much sense.
When Voyager discovers traces of a molecule, the Omega molecule, the Omega directive is automatically enabled. A classified mission to wipe out this molecule because one particle alone can rupture subspace and a chain reaction of several particles could destroy subspace in a whole quadrant, incapacitating warp travel in that quadrant forever.
First Janeway acts all secretive and tries to solve this problem alone, with only minimal information to her crew. Since Seven of Nine knows about this molecule already, Janeway involves her. Chakotay though convinces Janeway to give more information about Omega and her mission, so the crew can help her. Janeway thus assembles a senior staff meeting. Strangely, B'Elanna is not invited although she is chief of engineering. Although Janeway tells her senior officers to keep the mission classified, they all seem to be quite open afterwards. They talk about destroying this molecule on the bridge while not only senior officers are present but a bunch of ensigns, too. On the away mission several crewmen are directly involved and see and hear everything. At that point, Janeway could have just opened a channel to the whole ship and gave away all classified information which wasn't classified anymore anyway.
When they encounter a planet with millions of such molecules, which were used by local scientists to create an inexhaustible energy source, the crew beams those molecules into a containment chamber on the ship, neutralizes some particles and detonates the rest in space with a torpedo. I wonder how this detonation doesn't cause a chain reaction and blow up subspace. Quite illogical. And how comes, they can just beam those highly complex molecules to the ship and rematerialize them with no problem? Also, the alien scientists most likely will continue their research on those molecules. Why didn't Janeway offer them another technology to help them with their energy shortage? At least tell them that they are playing with fire. It's just a matter of time when there is the same threat again to the quadrant. And isn't that molecule said to be rare? Yet, those scientists obviously created millions of them.
