After the "Assault on Roswell" you destroyed the Alien Virus. at least you think you did !, it seems you yourself were infected and have become a carrier of this mind altering disease and are the unwilling host bringing the virus to your place of birth Portown...
Idea of using Daikatana-saving gems ruins almost everything... that plus ineffective weapons, high difficulty, no fun factor. Too bad, beacause I liked the screenshots and start of the game, music and secret areas.