The movie tells of a young girl, Mii, who lives by herself in a large mansion after her parents had disappeared.  The large plot of land (Green Field) includes a large tower where the young girl spends most of her time.  While going through her father's old work one day, she attracts a group of  Unown to the tower.  The pokemon hypnotize her to help her get over the grief of her parents' disappearance, convincing her that they are there to grant her a wish.  Mii, who had associated her father with the legendary pokemon Entei, asks the Unown to bring her her father back.  The alphabetic pokemon respond by creating an illusionary Entei to act as her father.  Mii then wishes for a mother, so Entei brings her Satoshi's mother, who had been in the area with her son. 

"Emperor of the Crystal Tower" was the #3 movie in Japan on its opening weekend.  At the end of the movie was a brief preview of Movie #4 and of the Nintendo 64 game Pocket Monsters Stadium 3. 

The American version of the movie had very little advertising (compared to the huge advertising campaigns that existed for the first two movies) and placed the lowest on its opening weekend of the first three movies.

From left:  Japanese VHS, feature; Japanese VHS, mini-movie;
American VHS, feature + mini-movie

Thanks to Pokemonica for the above staff list.