City of Titans is due to give us remarkable freedom over how we chose to play our character: Heroes, Villains, or somewhere in between. This freedom will be represented in the choices we make during the course of the game, but where do those choices come in with regards to the mission creator. Story lines can go in completely different directions depending on the players actions.
Scenario: Character happens upon an armored car that is known to be carrying a MacGuffin, and is currently being attacked.
Option 1: Help the guards -- The attempted thieves are taken to jail and the guards ask you to deliver the MacGuffin. This sets the players up on a series of quests that lead to the big bad that orchestrated the whole thing.
Option 2: Help the thieves. You acquire the MacGuffin and take it to whatever destination they had in mind. This leads to you working for the big bad for a while.
Option 3: Take out everyone and keep the MacGuffin (or sell it yourself). This leads to the big bad sending goons after you. It may lead to an eventual showdown with the big bad.
The fact is that most stories have multiple branching points, and the overall story will be vastly different based on the character choices.
The simplest way to create these would be to create multiple missions based on what decisions the character made in a previous mission.
The question becomes, how would you denote which missions in an arc a character has completed and which missions are available now based on those previous choices?
One option is to allow players to create a unique item that will function as a quest key. MacGuffin 1.0 and MacGuffin 1.1 may look the same, but passing them to an NPC to start a mission will lead to two very different missions based on which MacGuffin was used to start the mission. You could, likewise, use the item as a "required item" to start a mission if there is no specific NPC to speak with.
Another option would be to denote in the missions description which mission is the next appropriate mission based on you're actions. This may be the easiest to implement (as it would truly require no additional implementation). This does, however, contain a few flaws. You may end up coming into the middle of missions for which you have no context, or accidentally enter a mission that assumes decisions that your character did not actually make. Not to mention how incredibly immersion breaking it would be to have to pull out a flow chart to see which mission you go to next and the spoilers that may be present in such a chart.