Et af de mere kontroversielle aspekter af Assassin's Creed-serien har altid været de moderne dele af historien, som drejer sig om den moderne udgave af konflikten imellem Tempelridderne og Assassins. De moderne sektioner af spillene tog dog bagsædet en smule, efter at disse kom under skarp kritik fra fans, da hvad der bliver refereret til som "Desmond-cyklussen" blev afsluttet i Assassin's Creed III. Nu lader det til, at disse sektioner igen vil få et større fokus, da Assassin's Creed: Syndicate vil starte en ny moderne historie, som Marc-Alexis Cote har fortalt Gamespot:
"The Assassin's Creed series story is still going somewhere, absolutely. The overarching story is divided up into cycles. So we had what we called the Desmond cycle, which ended with AC3. Black Flag was the transition point between the Desmond cycle and the new cycle."
Ifølge Cote repræsenterede Assassin's Creed IV: Black Flag og Assassin's Creed: Unity overgangskapitlerne i historien, og derfor vil Assassin's Creed: Syndicate påbegynde en ny cyklus for den større historie:
"[Assassin's Creed 3] was the end of the Desmond cycle. And then we started up the new cycle, which I think will become much clearer with Assassin's Creed Syndicate, without spoiling it. I can't go into details about the present-day story, other than to say it is coming back, it is going to make sense for our players, and they're going to understand the conflict between the Assassins and the Templars."
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