An idea I had for an extra set of missions:
The tyrant invites a scientist/alchemist/mage/beast-tamer/whatever to work for him. The scientist shows up in a heavily armored caravan that makes its way across the map to the tyrant's castle. If he gets there, all the tyrant's units will be upgraded according to the scientist's discipline (new unit type, more armor, faster attack, etc.) But if the rebels manage to intercept the caravan and take the scientist to one of their own villages, they can benefit from those upgrades.
Have several of these caravans in the course of the game, each scientist having a different specialty. If you can get one of each, they will work together to create a super-unit to use against the tyrant (say, a giant siege tank with multiple flamethrowers, a massive warbeast with mounted archers to serve as a living ram, the aforementioned Project Odin...).
Needless to say, if every caravan gets to the tyrant's castle he gets the super unit too.