Each game has its own story line and together they form the story of the Assassin's Creed franchise. On this page, however, I only describe the story of the main games.
Assassin's Creed: Altaïr's Chronicles
Assassin's Creed: Bloodlines
Assassin's Creed II: Discovery
Assassin's Creed: Project Legacy
Assassin's Creed: Lost Legacy
The story is about a man, called Desmond Miles, who lives in 2012. He is the descendant of an Assassin line. In the beginning of Assassin's Creed, you learn several things about him. He was raised in a town called the Farm. Ther he was supposed to become another Assassin. He didn't like living on the farm thus he fled. He went to the city where he lived like a normal civilian, became bartender and got a motor cycle. For that last one he needed to give a fingerprint. On that print he was caught by an orginisation called the Templars.
The Templar organisation is an orginisation who are in power at that time using several Pieces of Eden's. These gifts came from Those Who Came Before, as said by Warren Vidic, a major Templar. The Templars force them in a machine called the Animus to locate a few of them. In the Animus he can relive the lives of his ancestors. In Abstergo, the Templar organisation where he's being held, he relives the life of Altaïr Ibn La-Ahad, an Assassin from the crusades.
Eventually, the Templars find what they want and they think Desmond is useless. Thus they would "take care" of him. Lucy Stillman, an Abstergo employee, appears to be an Assassin and saves him from death. Here ends Assassin Creed and it is also the moment when Assassin's Creed II starts. At the game's beginning, Lucy helps Desmond escape from Abstergo and brings him to two other Assassin's: Rebecca Crane and Shaun Hasting in an Assassin Hideout.
Rebecca has made a better Animus, the Animus 2.0 in which Desmond relives the life of Ezio Auditore da Firenze. He needs to relive his life because the Animus has a downside and a downside, it's for both the Bleeding Effect.
The Bleeding Effect makes the user more in sync with his ancestor. Thus you can learn his skills which Desmond definetly needs. But by doing so you can lose track in which time you live and you can get mental. This happened before by Subject 16.
After he relived a large part of Ezio's life, he meets Minerva who spoke through Ezio to Desmond. She told him that she was one of Those Who Came Before. That humanity was at war with them and that something happened none did foresee. This happening made sure there were just a few Humans and a few of Those Who Came Before left. She told him that they rebuilt, together, to make the future brighter. But soon it would happen again.
Ezio talking to Minverva at the Vault in Rome
Just after she delivered the message, the Assassin Hideout is attacked by Warren Vidic and his Templars. Desmond and Lucy defeat them and they can escape. After this, Assassin's Creed II ends.
Panoramic view of the Assassin Hideout
Assassin's Creed Brotherhood starts right where Assassin's Creed II ended, in the Vault. Ezio is helped by his uncle Mario, they escape together and Ezio told them what he had seen. They all believe him but don't fully acknowledge what happened since it went above their believes.
The Vatican Vault
Shortly after that, Monteriggioni, the city of the Auditore family, is attacked by the Borgia family, in particulair, Cesare Borgia and Mario dies. Ezio saves his sister and mother and sets for a journey to the city of Rome.
Panoramic view of Monteriggioni
Desmond is pulled out of the Animus 2.0 after that and they have to travel a bit. They go to the Sanctuary in Monteriggioni where he has to find a way into Villa Auditore together with Lucy. After that, he enters the Animus 2.0 again.
Sanctuary entrance view inside Monteriggioni
Cesare adressing his papal guards
Cesare Borgia escapes to Siena. Ezio tracks him down and throws him off a wall. After that, the future Assassins locate the Piece of Eden through Ezio's memories and Desmond is pulled out of the Animus 2.0. They set for Rome where th Apple, the Piece of Eden, is accesed through the Colosseum. They go there and they reach the Apple, which lies under Santa Maria Aracoeli, thanks to Desmond's new free run skils. In the Colosseum Vault, as it is named, Desmond takes the Apple and then the Apple orders him to stab Lucy with his hidden blade. Here ends Assassin's Creed Brotherhood.
The Colosseum Vault
The story continues in Assassin's Creed: Revelations were Ezio travels to Constantinople to reach Masyaf and find a hidden weapon under it. Desmond, in the future, will try to restable some important memories through means of a black room.