The generalities of the missions are discussed here: http://www.arcengames.com/forums/index.php/topic,9534.0.html
And a bit more about how the structure of the core missions will intersect with overlords and continents is here: http://www.arcengames.com/forums/index.php/topic,9538.0.html
But, if you look at the flowchart in the first post above, you'll see it also talks about "side missions."
IMPLICIT SIDE MISSIONS
Some of those are really unstructured, sandboxy things like you can do now. Just going out to get crafting resources and craft something new to use is sort of a side mission, although nothing in the game will label it as such. But in the flowchart node "Side missions" this is certainly a key component, since it's what helps you get ready to take on the core missions (or even other side missions), just as it's a big part of strengthening yourself now.
EXPLICIT SIDE MISSIONS
On the world map, you'll see little icons denoting side missions (and ones denoting your two core mission options, actually). Once you start one mission, you can't start any other missions on that continent until that one is completed or you give up on it. That's partly to keep multiplayer sane and avoiding some exploits there, but partly also to handle game flow even in solo play.
The difficulty of side missions will be far below that of the core missions, by the way. They're something smaller that will take place in existing regions (often which you'll have a lot of latitude in deciding how to solve the conditions of through multiple regions, actually), and they'll come with smaller rewards that are nonetheless really important to your civilization and its progression.
There will also be Persona-related side missions that are more story-centered and linear. These won't be recycled by the game, unlike the more mechanics-based missions, so once you've gone through the whole story of a given persona then that's it for that particular thread of side missions. But there will always be other non-persona-related side missions to take their place as the game progresses onward.
TIME EXPIRATION OF SIDE MISSIONS
At any given time there will be a number of side missions, and a lot of them involving things that help out NPCs in your settlements. More on that in another thread.
However, each side mission (unlike core missions) will only last for a certain amount of "time." We haven't settled on the terminology here yet, but for now I'll just say that a given mission would last for "X number of missions." So, each time you complete a mission (core or explicit side), that's one mission. If a side mission "lasts for three more missions," then when you complete any other mission it will then "last for two more missions" and so on.
Thus even the side missions have a heavy dose of opportunity cost to them. None of them last forever, and there will be enough that you can't complete them all. Figuring out how to min/max your progress through the side missions to best benefit yourself and your civilization is going to add a new kind of strategic planning to the game that it currently lacks, but this is something I'm quite excited about because it really allows for longrange planning in a way the game currently does not.
HELP YOURSELF OR HELP YOUR CIVILIZATION
One particular new sort of choice these explicit side missions will bring with them are choices between upgrading your own character, helping some specific NPC with their goals, or helping out your settlement in general. You can't do all the things all the time, so that's where some of the heavy opportunity costs come into play, making you make strategy-game-style choices. In Chess I can't move all my pieces at once, so I have to choose which move will best lead to the outcome I want on a given turn. Then next turn I do the same, etc. Each mission you undertake is kind of like a turn in Chess, in that grand strategic sense. Kind of like each planet you take in AI War, in the exact same sense.
Anyway, as one example, we're planning on level-gating when spell recipes become unlocked for your use. However, if you really want early access to some specific spell before you'd normally be able to craft it (which could be really helpful for taking on some core mission that's giving you trouble), then you could pursue a side mission that lets you unlock that spell early. There's a lot of potential here for all sorts of interesting, difficult choices.