This second movie continues where the last left off and is based on the first book of a three part novel series written by Kenji Tereda who was the main scenario writer for the TV series (he also wrote the scenarios for JRPGs Final Fantasy I - III too apparently). So again, this isn't based off Izumi Matsumoto's original work. It continues to show how he envisioned the characters from the original Manga, now nineteen, would have moved on with their lives through university. If you watched the first movie, you might feel better for the characters after watching this. Maybe it was Tereda's way oftrying to redeem himself after the poor reception of the first movie. I guess you could also consider this movie fan service for those who wanted a more complete closure to the relationships.
However, it gets quite weird with the supernatural powers back in and the way they're used just feels silly as usual.