In the two-part episode "Scorpion", Captain Janeway foolishly aligned Voyager with the Borg. This seemed insane at the time and now a little over a season later, the implications of this insane decision have come back to haunt them.
Voyager has picked up some transmissions in the Delta Quadrant that SOUND like they are Starfleet but cannot be. When Tuvok and Chakotay beam down to investigate, they find a copy of Starfleet! It looks awfully exact and they plan to go back to Voyager to tell the Captain. However, they are discovered in an off-limits area and a guard tries to capture them--so they disable the guy and beam back to the ship. There they realize that he's actually species 8472--a rather frightening looking being who has somehow assumed human form. Why have these guys created their copy of Starfleet headquarters? Well, it's obvious because after their encounter with Voyager, they feel at risk and this could be the prelude to an attack. How can they resolve all this paranoia and preparations for war--especially since Voyager stoked these fires.
This is a very fascinating episode and I thoroughly enjoyed it. My only complaint, and I mention it in the summary, is that all this paranoia sure seems to work itself out awfully easily. Still, a dandy show.