Throughout the game, Ezio takes on various missions that bring him closer to the Apple, Cesare and Rodrigo, from helping keep the local Courtesans (an early version of what we know as prostitutes) safe, to killing Borgia captains and destroying the inventions of Leonardo da Vinci. While da Vinci is still an ally this time around, you learn that he was forced to create weapons of destruction (based on da Vinci's actual inventions) or die.
As you continue through the missions, there are several side quests that you can complete in order to earn more money and experience. Collecting feathers is once again present (although there are only 10 of them this time, instead of 100), as is collecting Borgia flags and Keys of Romulus. The Keys of Romulus are similar to the Assassins Seals from II, and when you collect all six, you unlock the Brutus armor (I highly recommend doing this). One other concept that was added in this game was recruiting assassins. Throughout the game, you will get the chance to recruit regular citizens of Roma that are being harassed or attack by the Borgia soldiers. Once you have saved them, they will automatically join the Assassins Guild and can be sent on missions to collect money, experience and rare items. Plus, they can be called upon to assist you in fights or in any situation where it's necessary to get rid of soldiers. They are extremely effective in attacking the soldiers, and they definitely come in handy in later portions of the game.
The glyphs are once again available in this game (only 10 this time around), and completing all glyph puzzles takes you to a brief climbing mini-game that puts you face to pseudo-face with the notorious Subject 16, and also gives you more information what the Animus tests really prove.
Once you begin your final descent in the game, you wind up face-to-face with Rodrigo Borgia once again, and have to stop Cesare in order to get the Apple back. Going after Cesare requires chasing him back to Monteriggioni for the final battle. Without spoiling too much, Ezio winds up killing Cesare. In the process of this, Desmond discovers through a glyph the location of the Apple (the reason he and his friends are in Monteriggioni in the first place), which leads Desmond to the world-famous Coliseo for the final search. While on the search, Desmond begins hearing messages from Juno, a similar being to that of Minerva from Assassin's Creed II. He and the crew finally find the Apple, but do not know how to activate it. Desmond touches it, which turns out to be the activation key. It freezes time around him, and we once again hear Juno's voice: