The third act is unfortunately pretty typical of Voyager- a contrived action/threat sequence not really warranted.
However, I think the writers were perfectly aware of this. The script is very meta and self mocking. Tom literally says at one point "who writes this stuff?" and in other parts, they debate how a story should progress.
This episode also shows us a glimmer of the type of conflict between Starfleet and the Maquis that should have occurred in the first season or two. Unfortunately, Voyager almost entirely tossed that aspect by the first episode after the pilot.
However, I think the writers were perfectly aware of this. The script is very meta and self mocking. Tom literally says at one point "who writes this stuff?" and in other parts, they debate how a story should progress.
This episode also shows us a glimmer of the type of conflict between Starfleet and the Maquis that should have occurred in the first season or two. Unfortunately, Voyager almost entirely tossed that aspect by the first episode after the pilot.