Though I'm not sure they were aware of this at the time it was written, they honestly didn't need much of an end game since Heroes Reborn would essentially wipe all of that away anyways.
Heroes Reborn came about a year and a half after they began The Crossing (which was responsible for a significant decrease in sales. Most titles had been doing fine before the Crossing, and Harras, Kaminski leaving their titles). I might be wrong, but I don't think they planned anything with Heroes Reborn as their reboot button. Although a big fan of the period (and actually having fondness for the Crossing), I honestly beleive it was poor planning.