I see the final enemy as something much more abstract. I think that Suikoden III's ending gave us the best foreshadowing of what this can be.
Suikoden has always been about the battle between Order and Chaos, something that Leknaat acts as a third party to by ensuring Balance between the two. This concept shackles humanity, making people slaves to destiny and unable to choose their own fates. Luc, despite the error of his ways, sought to free humanity from these shackles. It is necessary for this Balance to be destroyed, something that Leknaat might stand in the way of. Though, that's questionable considering how little she did to convince Luc otherwise. It could just be that she didn't believe him to be a big enough threat.
In doing so, however, the Stars of Destiny would cease to exist.