If you've created a new city, you'll probably want to delete the original missions because they won't match your new landscape. If you just delete everything from mission.ini, or just delete the file, the game won't load. Ben Millard wrote the bare minimum code required to load a level with a player, multiple cars, and open the Grrrrand Theft Auto!.
You can rename the INI file in the archive to "MISSION.INI", but I do not recommend doing this if you have standard cities.