Assassin's Creed IV: Black Flag

In this game, a woman comes to you when you're out of the Animus and tells you that the head of Abstergo Industries, Olivier Garneau, had a meeting in Chicago (where Watch Dogs (2014) takes place) but hasn't returned. In one Watch Dogs side mission, you kill Garneau. Should the player then decide to profile Garneau with Aiden's phone, his descriptor even reads "Targeted by the Brotherhood" clearly referencing the Assassin brotherhood in these games. This puts both games in the same universe.

In the present-day setting during the game one of the computers you hack shows Desmond Miles' ancestors through his mother and father. This report indicates that the first playable ancestor, Altair Ibn La-Ahad, comes from his mother's side. It shows the second one, Ezio Auditore Da Firenze, on his father's side. This contradicts the original statements made by Ezio and his uncle, Mario Auditore, in Assassin's Creed II that they were indeed descendants of Altair. This was either a mistake in writing or a change to the canon of the series.