Unmarked spoilers below.
- The mission "Kyrie Eleison". Shay has been tasked with retrieving a Piece of Eden from a Precursor site in Lisbon. After some puzzle solving in the church, Shay opens a secret passageway to the Piece of Eden. So you just grab it and head back to the Bureau, right? WRONG. The minute Shay grabs the artifact, it disintegrates in his hands, and the ground begins rumbling. You go back up to the church, only to find the whole city of Lisbon falling down around you. From that point, it's a mad dash to get back to the Morrigan before Shay is crushed by the falling buildings. It's only after Shay's back on his ship when you realize that you, as the player, inadvertently caused the 1755 Lisbon Earthquake.Crew member: How could God do this to them?Shay: God had nothing to do with this.
- This mission also gives us a very chilling Non-Standard Game Over; if Shay stands still for too long while the city falls apart around him, a special Game Over cutscene will play showing him being buried by falling debris.
- While Shay makes it out alive, many citizens don't. An attentive player can see people crushed by falling buildings, burning to death in the ensuing fires, see people try to help injured before the ground breaks under their feet. Every time Shay comes to a plaza, you can hear a baby cry among the screams of the people.
- Finding the headless horseman can be quite a surprise for those who find it by complete accident, especially since it only spawns during certain circumstances, making it possible to not know about it even after spending time near the area. There's only two valid ways that it can die. Either by fall damage or by shooting a pumpkin on the church's graveyard. And, well, some glitches. Of course, knowing about it beforehand greatly reduces it's creepiness.
- One of the audio files that you can find in the Abstergo office (practically at the start of the game, since its in one of the terminals near the player's) you will find that the Templars are in the Caribbean seeking to dig out the Observatory.
- The concept of this game has its fuel - an Assassin turns and joins the Templars. Despite the fact that the series runs on Grey-and-Grey Morality, in the course of the series, the worst atrocities have consistently been at the hands of the Templars. And now, not only is an Assassin - an Assassin we are playing and seeing the world through - joining them, he proceeds to not only turn against and kill his former fellows among the Assassins, but by the final scene, shows that he has come to completely embrace the Templar beliefs and reject those of the Assassins. And you can't stop it, you're just dragged along for the ride.
- Berg uses the footage of Shay Cormac as a way to sow discontent among the Assassins. And how does he reward you? By giving you a choice. Join the Knights Templar, or get shot on the face on the spot.
