Altair and Ezio
Although Ubisoft has not confirmed anything yet creative director Patrice Desiliets has said that there will be an Assassins Creed III. This installment will see Desmond become the ultimate assassin.
"Assassins Creed is story of one man relieving the lives of his ancestors. Altair was the middle of a very very long timeline. There are still many places to explore"
“Assassins Creed has always been planned to be a trilogy, and Desmond is going back in time, using the Animus to eventually become the ultimate assassin.”
-Patrice Desiliets
At E3 2009 he exclaimed “I’m telling you. At the end of AC2 you’ll say‚ ‘Holy crap, I never saw it coming!’ There will be a cliffhanger. It’s cool to have a cliffhanger,” that leads into Assassin’s Creed III. As for the writing on the wall Patrice says “It has nothing to do with Assassin’s Creed 2, it has to do with the Assassin’s Creed universe, not the second one.”
More recently as Patrice was wrapping up production on Assassin’s Creed II’s in September he mentions he’s looking forward to rounding out the trilogy. “I have many different ideas. I’m not ready yet to exploit them. I think I have some juice left in me left to continue this. I’ve been doing Assassin’s Creed games for the past six years. It’s tough to be bored. I was a bit bored with the Turk crusade and the monk aspect, and everything, but in this there’s a brand new setting. And it’s my first sequel; I never did a sequel before, because I didn’t do any Prince of Persia sequels. I love the idea of refining your ideas, the gameplay and what you can do with it. So I’m not bored yet.”
Setting
Assassin's Creed III may either see Desmond still in the Animus, or fully independent of the Animus and taking the fight against the Templars to the modern day. If the game continues in Desmond's genetic memories, there are many possible settings for AC III. Here are some possibilities.
World War II
Assassin's Creed III could be set in the Second World War. Ubisoft has already stated that they are looking into the possibilities of a World War II setting and having an female Assassin as the main character. Further leading to the idea is that according to Subject 16, both Adolf Hitler and Joseph Stalin were confirmed to be Templars. Franklin Roosevelt was also seen holding the Apple and Altair mentioned in his Codex a vision of the Atomic Bomb. Possible missions could be the many failed assassination attempts on Adolf Hitler or fighting for Pieces of Eden with the Nazi Occult. Support for this time period is found in-game as a message left by Subject 16 refers to Hitler going missing with PE4 (the fourth piece of Eden) when he was supposed to be faking his own suicide and passing the piece on.
The New World
In the Vault, Minerva mentioned Temples that held great significance. These Temples could very well be the Aztec, Inca, or Mayan pyramids that are all across Mexico and Peru. Fransisco Pizarro was also confirmed by Subject 16 to be a Templar, so the idea of Conquistadors as more than just treasure hunters is not too far off for the Assassin's Creed universe. Crystal Skulls were also mentioned by Abstergo in the e-mails so a New World setting would most likely be the Templars and Assassins hunting down the Crystal Skulls.
Japan
Japan is also a possible setting for the third Assassin's Creed. The messages left by Subject 16 show Asian architecture and even one says "YONAGUNI". Yonaguni is the westernmost of the Japanese islands and is home to the Yonaguni Monument, a large underwater rock formation that has been said to be man-made. This could be a building of some sort left by Those Who Came Before. Adding to the probability of a Japanese setting is in the short video The Truth. In the background, the mountain looks remarkably similar to Mt. Fuji. This could be coincidence, especially since it does have notable differences than the actual Mt. Fuji, (Mt. Fuji has a larger base and a sharper peak) or it could prove that Japan plays a major role in the Assassin's Creed Universe.
Character Development
The cliffhanger at the end of the game leads us to ponder about what will happen to Desmond, Lucy, and the other Assassins as well as Vidic and the Templars.
Desmond Miles
Desmond will probably develop into a true Assassin and be completely free of the Animus, completing missions in the modern day. He already has a hidden blade, and used it with great skill defeating the Abstergo guards, so it will be interesting to see how he develops as a character in AC3. Another likely idea is that Desmond and Lucy will fall in love, as it is becoming more and more obvious that both seem to share feelings for each other.
Lucy Stillman
Lucy's role in the grand scheme of things is still pretty vague, so it is hard to predict how she will end up when the cards are all down. However, it is obvious that she will help Desmond the entire way and that she will most probably become his love interest.
Warren Vidic
Despite being the scientist apparently responsible for the Animus tests Vidic appears at the end of AC II in what is potentially a very dangerous situation, hinting he is more than just a scientist. As his true role in Abstergo, though apparently high up, Vidic will most likely be the primary antagonist for the parts of AC III that are set in Desmond's time.