Anonymous: <p>You know I think I've figured it out. What Sam meant at the end of Legacy when he said "You were right about everything." It's the payoff to their previous interaction where Sam is criticizing Alan for believing Flynn is still alive, planning on changing the world, not abandoning Sam willingly, and physically still located at Flynn's arcade.</p>

Good point. Alan did turn out to be right about all of those things.

Sure hope he got a bit more clarification from Sam afterwards, though.