At the end of AC3, Desmond and William confront Vidic and Desmond says "It's all over, doc!". Then, Vidic says "Desmond, do it." and Desmond quickly stabs his dad William. It is then revealed that during Desmond's time at Abstergo, Vidic implanted an impulse in Desmond's mind to kill William Miles, just like he did to Daniel Cross to kill the mentor. So all this time, Desmond was secretly a sleeper-agent. Desmond then smiles at Vidic and they both walk off as we hear the Templar attack being launched in the background and the credits roll.
I'm not saying I want this to happen, but wouldn't it be the biggest mindblow ever?