Darwinia is composed of a set of independent maps. When you complete one map, all maps depending on the one you completed are unlocked and may be started at any time. Aside from trunk ports allowing you to choose a new angle of attack, and research progress based on the amount of time spent on a mission, there is no interaction between regions.
Each region has a set of primary and secondary objectives. A primary objective is required to unlock the following missions in sequence, while a secondary objective may make future missions easier (although there is no guarantee.)
Ultimately, you want to remove the infection from Darwinia. Even if you lose forces, it is not much of a permanent loss since you can recreate them. However, if you fail a mission, you can reset the region back to the beginning when you first explored it.