Well, here I have two youtube vids that show the ending, and some quick explanation:
Spoiler:
During the game you find out that your master in Masyaf is the true evil mastermind behind all the Templars, and you have all along been doing his dirtywork, so that he would be the only one who knew of the Artifact (forgot its name, something with Eden). The Artifact has the ability to bend every human who is nearby to the will of the person who has the Artifact, basically he wants to be ruler of the World. So in the end there is a showdown between you and him, After the fight the present day scientists are able to use the Eden to locate where all the other Artifacts are located on Earth. Watch the two youtube vids:
Both videos contain major plot spoilershttp://www.youtube.com/watch?v=CuhGhC-J0-ghttp://www.youtube.com/watch?v=DzBNI4pmbXUThey ending of the first one overlaps the start of the second one.
Also, there is a lot of speculation of the stuff at the ending that can be worth reading here: http://www.computerandvideogames.com/article.php?id=175552
There's a lot of interesting plot being told through e-mails, especially the classified ones, that I haven't been able to locate here. Among other things we have heard about
Spoiler:
other subjects like Desmond, some have used the Animus too much and have gotten their identity mixed with their Ancestors, we also heard about one who had a "ship" of sorts that could time-travel, and so on