Assassin's Creed Unity's co-op missions are entirely separate from the main story, the idea clearly being to avoid upsetting the hordes of players that have grown up with the franchise's staunch solo approach to its campaigns. People seem to get annoyed when popular games change too much, after all.
Co-op missions are designed with an ideal player count in mind, but you're not forced to undertake them with a specific party size. You can tackle a four-player mission with just two players if you like, or even go solo. Or a team of four can attempt a mission made for two. It's entirely up to you, but bear in mind that the rewards don't scale depending on numbers - a four person team that beats a two player mission will have to share XP and loot drops designed for less. On the other side of the coin, a solo player that manages to best a four player mission will enjoy a reward for four as payment for a tough job well done.
To what extent you want to work together is down to you, although if you're the kind of person that wants to stay undetected then co-operation is key given the increased enemy count in co-op missions. At the very least you'll want to make sure each person on your team has a different 'active skill'. These include the ability to heal yourself and others, temporarily seeing through walls in a bid to locate guards, disguising yourself as the enemy and carrying a cache of extra bombs and other items to dish out to anyone in need.
Which abilities you choose to mix and match will likely depend on the objectives you're taking on. Our Notre-Dame mission took the form of a heist, the goal being to steal a treasure hidden in the catacombs from under the noses of the guards stationed there to protect it. Others include assassination attempts and protection jobs, although details are rather thin on the ground as to exactly how many categories will be present in the full game.
Further customisation of your skill set is performed by defining what kind of gear and weapons you want to equip. Essentially you build your abilities around four basic approaches: being 'deadly', 'resilient', 'unseen' or 'agile'. It is possible to spread your bets in an attempt to achieve a well-rounded assassin, but if you decide to play co-op missions frequently then it's probably a good idea to co-ordinate with your partners and each specialise in a different area. It's also worth noting that it's supposedly impossible to max out all areas, eventually forcing you make a decision about what kind of assassin you want to be.
Our Notre-Dame mission lasted around 15 minutes, but we're told that other heists are balanced to last for over an hour. It's these lengthier examples in which famous faces of the French Revolution era that don't make an appearance in the main story will be found. Clearly, that's going to be more or less appealing depending on your knowledge and interest in the setting.