According to historian Shaun Hastings, there is a gap in Ezio's timeline. Though data from the Animus is sparse, it would seem Ezio discovered a strange artifact in 1506, while on his way to Navarre to fight Cesare Borgia.
The artifact in question was held by a group of Templars plotting to overthrow Queen Catalina, off the Spanish coast. During the night, Ezio boarded the ship, overcame the Templars, and set the vessel ablaze. He then stole the chest holding the artifact and, once in a safe place, opened it. The Animus readings are very erratic after that. To quote Shaun: "Bugger if I know how DNA and an earthquake are related, but this looks like readouts from the Richter Scale!"
Acording to our data, Ezio's timeline seems to jump to the end of the 16th century - with him fighting against several strange, powerful foes. This cannot be possible. Immediately afterwards, Ezio appears, in 1507, sailing for Navarre. I guess the truth will remain a mystery.