Lucy died in Assassin’s Creed: Brotherhood, and in Assassin’s Creed 3, Desmond sacrificed himself to protect the planet from a solar flare that would have caused the Second Disaster.
The ending to the third Assassin’s Creed game was originally intended to end quite differently, according to interviews with staffers that worked on the titles and conducted by a Ph.
The game was followed by Assassin’s Creed: Rogue, which takes place between Black Flag and AC3.
According to de Wildt’s paper (thanks, Eurogamer), the original plan for the trilogy ending was pieced together based on interviews with Assassin’s Creed creator Patrice Desilets and Assassin’s Creed 3’s creative director Alex Hutchinson.