I would have decided that the Enterprise encounters a dead Cube. There is no power and all the Borg inside are dead. After an investigation, they realize that there is a deadly species that not only resisted assimilation, but dealt the Borg a heavy blow militaristically.

It would be the season 6 cliffhanger in place of Descent, basically Voyager’s Scorpion but several years early. Though it would probably result in Seven of Nine never becoming a character.

Another idea I’ve had recently is a system of worlds that are thriving and even more technologically advanced than the Federation. The catch is the Borg come by every stellar year and cull large numbers of people in exchange for peace.

We get a flashback to thousands of years ago when the Borg were not monsters but just augmented humanoids. They approached this species when they had just discovered space flight and offered their enhancements as a gift. Some accepted and others did not, causing a schism. Somehow, as the Borg became more forceful, the ones who rejected assimilation reached a deal which let the Borg take their sick and infirm and criminal class in exchange for leaving everyone else alone.

Obviously, the status quo is found to be untenable and Starfleet steps in to push the Borg out, making enemies of the new race. Stargate Atlantis did a story like this with the Wraith.