Subject 16 is another guy which actually same like desmond .. decendent of Altair, tangkap by Abstrego .. and held in the Aniums ..
in short subject 16 alrdy mati... after long used of Animus..(remember Desmond in AC2? he get some illutions?) subject 16 fall in coma and dead (physicall body buried) but.. part of his memories still located in the Animus backdoor (that island where desomnd meet subject 16)

if not mistaken.. during AC1 and AC2.. if u go check the Animus email.. Subject 16 keep sending in Emails to help/direct desmond

btw... Desmond is Subject 17 (if i not mistaken) 

summary story of AC1 -
That old man Al Mulim, assign Altair to kill 9 templars..
Al Mulim saids that the 9 target is Templars... some ting like tat..
after Altair killed 9 target.. he only realize the plot behind.. Al Mulim cheated Altair, the 9 target is not templars... some how is not suppose to kill...
so Altair go back and confront Al Mulim... only realize that Al Mulim want him to kill the 9 target to obtain the piect of Eden (apple) and bla bla bla and i kinda forget how it actually ends alrdy...

anyway ... part of the stories continue in ACR lor... (enter the memories of Altair by the 5 keys..)

base on the story... there are total of 6 piece of apple.... scarter around the world by the 1st civiliation...

The one that Altair get is from Al Mulim... he hide it in the Libary (we access in the end of ACR)
The one that Desmond get is from ACB ... Ezio get it in AC2 ..

er.. more info u can try read up .. http://assassinscreed.wikia.com/

if u want to know more about Ezio... the Encyclopedia edition got free one DVD .. after Ezio discover the Libary..
i read the story.. some how he giv up being Assassin.. and together with Sophia.. with 2 children... but den .. he still kena hunt by Templars ... and the stories goes on.. some ting like tat....

=/ he dead at age 65 heart attack...