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Assassin's Creed 3 introduced co-op to the series with a new Wolfpack mode. Ubisoft had been considering co-op for the series long before AC3, though. Mission director Philippe Bergeron says that they tried to include it in the first game.
Bergeron told OXM UK that co-op was going to be a "huge" part of the first AC. The game would've supported drop-in/drop-out co-op so a friend could hop in and help you assassinate a particularly difficult target. Eventually, though, this cooperative feature was cut because the game's engine didn't support it and it didn't fit the storyline.
"There was no way to reconcile having multiplayer or co-op in an ancestor's memories. Your ancestor lived his life in a certain way, so assuming you had branching storylines, it creates a paradox. It didn't fit."
If the problem with co-op was due solely to the story rather than technical limitations, I think Ubisoft could've made the feature work. The idea of people invading each other's ancestral memories isn't too much of a leap for the storyline. It's not like the rest of the plot is firmly rooted in established science. The Animus is basically just a magic chair. Players wouldn't have revolted if we learned that the Animus had a "tandem memory synchronization device" (or whatever the fuck) that allowed for an additional player to participate in Altair's memories. We'd just be happy to have co-op.
Ubisoft admittedly found a good story excuse for multiplayer, though. The online modes in Assassin's Creed Brotherhood, Revelations and AC3 are designed as training exercises for Abstergo, the villainous corporation opposing our heroes. It's a lot less silly than a "tandem memory synchronization device" but the downside is that players have to go it alone in the actual campaign. If you want to hunt down A.I. targets with friends, your only choice is to play the four-player Wolfpack mode with standalone maps.
It'll be very interesting to see what Ubisoft does with co-op in Assassin's Creed 4, particularly if it's a next-gen game. Will the improved technology encourage Ubisoft to integrate co-op into the main campaign, or will the series' multiplayer and single-player remained walled-off from each other?