It's not nuts. It ties the story of Altair and Desmond together quite nicely.
Desmond is captured by Abstergo, the head of the modern Templars. Since he is a decendant of Altair, they need him to find a piece of Eden. If you hack all the computers and such, it reveals that the Templars plan to use a piece of Eden to brainwash everybody, much like they planned to do to the Holy land during the crusades. They need Desmond because they lost their piece of Eden to a terrorist attack, most likely assassains. They force Desmond to use the animus long enough so that they can access the final memory; an image of earth with all the Pieces of Edn marked. Once they have this, the lock Desmond back up and leave him to his own devices, because he is no longer needed. This is where you see the prophetic messages, a result of the "bleeding effect" giving Desmond eagle vision. This messages were most likely left by the last test subject, who also is important(Do no know why).
On the surface Assassains Creed is just a hack and slash targetted at the frat boy majority. Beneath that, it is actually pretty deep, with conspiracies that link the past and the future quite nicely.