Historical: The facts we have are these: there is a great destruction involving the enemies of the Nephites, and the wicked were destroyed and the righteous preserved. In the end, the City of Nephi continues. It was "deliver[ed] out of the hands of their enemies."
These cryptic remarks allows us to reconstruct a major Lamanite military action that was taken to the City of Nephi. Where other actions might have occurred in the lands surrounding the city, it appears that this action occurs within the city itself. The primary reason for presuming this is that there was a large destruction of people. A military action involving only warriors would result in casualties, but not in anything that would be given as the destruction of a large number of people.
Additionally, we note that it was the "more wicked part" of the Nephites who were destroyed. This group is contrasted with the more righteous part, who were preserved. To understand the inferences of this passages we need to understand that Amaron is writing after the fact, and from the perspective of the survivors. No military action could have been precise enough to have singled out all of the "wicked" and ignored all of the "righteous." The story of the stripling warriors told later in the Book of Alma is remarkable precisely because it was an exception to the general rule of combat. Casualties are expected, even among the righteous.
The probable cause of the disparate destruction lies in the nature of the "more wicked part." If we return to Jacob's discourses and their probable target, Jacob is addressing those of the city who have become wealthy - and likely powerful. In the reading of the situation presented, this element of Nephite society gained political ascendancy during Jacob's lifetime, and while the religious atmosphere had returns to righteousness, there were yet great pressures away from the religion preached by the Book of Mormon prophets. With the integration of religion into society, we may expect that in addition to competing political systems, we have the beginnings of competing religious systems, and that the wealthy and powerful were espousing some other version of religion than the one that Jacob and Enos (and the other prophets) preached.
Nevertheless, there are adherents of the true gospel. Those do not appear, however, to have been among the rich and powerful. Thus there appears to have begun a social separation in religion that mirrored the social separation of wealth that Jacob preached against. It is this duality of social structure that allows us to explain the way in which only the "more wicked part" of the Nephites were destroyed.
First, it is imperative that the fighting occur within the confines of the city itself, as many of the powerful would not likely be among the warriors fighting in the field. Secondly, the target of Mesoamerican warfare was not destruction, but dominance. In the process of dominance, the conquerors would capture the leaders of the community and remove them as captives of war. In later Mesoamerican societies, these captives were the subject of public humiliation and usually ritual sacrifice.
In this scenario, the city of Nephi would have been invaded by the Lamanites, and most of the powerful of the city would have been take away captive. This effectively is described as a destruction, for they were no longer present in the city of Nephi, and many could have been sacrificed after their removal. The lesser economic/political status of those that were seen as "righteous" would have preserved them from the capture, because they did not carry the same prestige as the rich and powerful. Thus this social/religious distinction that developed in the city of Nephi becomes the basis for understanding the divergent fates of the "wicked" and the "righteous."
It is also very predictable that after the survival of the "righteous" that a religious revival would have occurred, where the remaining group would have recognized their salvation, and any others who remained would have undergone a repentance process as part of their process of recovery from the invasion.
We have so little information here that filling in the gaps is necessarily speculative. Using later Mesoamerican practices as our model, we may reconstruct this episode in the city of Nephi as follows:
This background explanation for the social factors surrounding the City of Nephi will become even more important later in the Book of Omni when Amaleki records the exodus of Mosiah and the righteous from that city.