Cubsfan- I’ll try to explain as best as I can (it’s been a while):
The first time you fight Rodrigo Borgia, in Sequence 11, is the last major turning point of the game. Ezio meets with his allies, who turn out to be Assassins, and officially joins the order.
Sequences 12 and 13 are DLC-only mini-adventures that aren’t absolutely required, but do add some minor characters and flesh out the story a little more (and also have a fun little free-flying area, where, incidentally, you can also pick up the Flyswatter trophy if you didn’t get it earlier). It’s possible to play them after completing the game if you buy them then (I did), but the story is most definitely not over at this point.
Sequence 14 is the big showdown against Rodrigo Borgia, and, as typical for an AC final boss battle, a doozy. First is the big fight to get to his doorstep, then a tricky stealth sequence to the Sistine Chapel, and finally, an air assassination right on him…
…which isn’t enough, of course. Now you have to fight him with the help of your shadow clones. It’s going to be a grueling fight, but eventually, victory is yours…
…no it isn’t; he gets right back up and stabs you in the gut! That’s it for you…
…no, don’t be silly, it’s a Fission Mailed (look it up! :D). You confront the Pope once more get to beat him for real this time. And then, after learning the true purpose of the Vault, then, finally, you’ve triumphed.
Oh, as for that little skirmish with the Abstergo guards while the credits are rolling…if you haven’t noticed, these games have really, REALLY long credit sequences. Apparently UbiSoft found it just as tedious as most of us, so they gave us a little something to do to break up the monotony (as well as showcase how far Desmond Miles has come).
So, actually…yeah, you’re already done.
That help? 