An Assassins Creed Unity DevBlog posted yesterday goes into the details of the game's "Paris Stories" side missions: what they are, how they connect to the main storyline and how the player can find them.
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Unity writer Russell Lees explained that the narrative basis for these Paris Stories is an order given to Arno by the Parisian Assassins. He is told to make living conditions better for the city's residents during this political upheaval. That's largely the end of the side missions' connection to the main storyline, though. The Paris Stories are meant to be able to be completed at any time, so they can't connect too much to a specific point in the primary narrative.
There are a few moments where the different stories overlap. For example, a main character that Arno meets in his main quest can become the leader of a new line of side missions. For most of them, though, Arno will be able to initiate new lines of side quests just by exploring the open world of Paris. If he's lucky, he might be able to come across mission givers just by keeping an eye out while walking around.
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For a more surefire method, though, Arno can also pick up newspapers placed around the city to see if there's any information he can use. Sometimes reading a newspaper article will place a checkpoint on your map that you can investigate to start a new side mission.
The Paris Stories, Lees explained, are all inspired by historical characters and events in Revolutionary Paris. As opposed to a game like Assassin's Creed III, where the plot of the game mostly follows the plot of the American Revolution, Unity uses the French Revolution more as a setting than a main storyline. The Paris Stories, then, are the writers' way of still utilizing all of the great historical stories that this period of Paris has to offer.