
The mission progress is saved in the global Clonk configuration (which is stored in the Registry on Windows). Each mission adds a password to the configuration which unlocks the next scenario. You can enter these passwords manually by pressing Alt-M while on the scenario list. The passwords are listed [here](
http://wiki.nosebud.de/wiki/Missions-Passwort).
Edit: Here's a translation:
Password | Unlocked by | Unlocks
----------------|-----------------------|--------
SkullGone | The Treasure | Frontier
NewLand | Frontier | Rattlesnake Canyon
RattledOut | Rattlesnake Canyon | Funnel Valley
Fenella | Funnel Valley | Regeneration
BackToLife | Regeneration | Sky Village
Speckles | Sky Village | Pearl Diving
Glint | Pearl Diving | The Last Will
ReachedTheOcean | The Last Will | Up High
TheClouds | Up High | Thunder Rock Mountain
ComeDown | Thunder Rock Mountain | Submarine
Aquagold | Submarine | Deep Down
TheAbyss | Deep Down | Seven Keys