I like the idea of using the Borg and some of the DS9 story line. One possibility for a story would be to pick up were DS9 left off.
Let’s say it is a few years after Sisco leaves to be with the Profits and Voyager has returned formed the Delta Quadrant. Kira, now the commanding officer of the station, is going about her daily routine when suddenly Sisco appears in front of her. Going against the will of the Profits, he is back to bring a message of warning to the Federation. The Borg have developed a new dooms day weapon, and are on their way to the Alpha Quadrant.
Using the powers of the Profits, Sisco has learned of away to finally defeat the Borg. He has learned the location of the Borg home world. By destroying the central link in the collective, the Borg will be destroyed once and for all.
With this story line we could bring in both the Enterprise-E and Voyager, with the two captains with the most Borg experience. We could also bring in the Klingons, Romulans, and even the Dominion.