In Titan A.E. the human race is able to create a new planet, New Earth (Planet Bob). What's stopping the Drej from just destroying that planet too?
The only thing I can think of is that the Drej ship that was destroyed at the end was the only remaining Drej left.
In the film's novelisation we learn that the hive-ship is in fact a colonisation ship sent from the Drej's home galaxy to the Milky Way. They intend to use it to exterminate all of the biologicals in the vicinity, then incubate a very large number of Drej to populate the (now empty) galaxy.
The basins holding the white dwarf were fashioned from energies whose properties could not be found naturally in the universe. They had been painstakingly worked out by the Drej over millennia while in their home galaxy—the plans for these properties, alas, had not been included in the matrix for the new ship from which Susquehana reigned.
The problem was that the Artifact had been damaged during the destruction of an early Drej colony. A suicidal pack of biologicals had blown up most of the planet to do so. The result had been less than they would have hoped, for the Artifact still functioned. But the Artifact had been damaged. The energy basins surrounding the white dwarf had become—for want of a better term—misaligned.
Unfortunately, Drej philosophy being what it was, no one had considered that the irreplaceable Artifact could ever be damaged. The Drej colonization project had been provided with a powerful Artifact, but no theory on repair or creation of new ones, since there would never be a need. And there was no way to contact home for repairs. The thought had apparently been that, without the theory, an enemy could never duplicate their greatest weapons.
With the Drej's colony ship destroyed, with any remaining scout ships unable to contact their home galaxy, without significant weaponry and without the ability to create additional Drej, New Earth (Planet Bob) is safe and sound for the foreseeable future.
