Assassin's Creed first introduced the Brotherhood's modern-day Desmond Miles storyline.
The original game alternates between the medieval adventures of Altaïr Ibn-La'Ahad and the modern-day experiences of Desmond Miles. Abducted by the Abstergo corporation, Desmond is connected to the Animus, a machine that lets him relive genetic memories from an ancestor.
This framing device establishes the series' two-layer structure: historical events are explored through a playable ancestor, while the modern plot reveals that Abstergo is connected to the Templars. Desmond's sessions also provide information needed by both the corporation and the Assassin cause.
Assassin's Creed II continues Desmond's modern storyline and expands it substantially, but it does not originate it. The Animus, Abstergo, Desmond, Altaïr, and the Assassin-Templar conflict are all introduced together in the first main game.