Chapter 4: What is the main plot of AC (The trilogy)?
The story is about a secret organization which kidnapped Desmond, with the intention of using him as a test subject in the Animus. Though it seems random at first, it is revealed through the course of AC1 that Desmond was specifically chosen because of his ancestors. The theory is that each ancestor leaves their memories in their heirs. Thus, by using the Animus, the organization is bent on extracting those memories to find a certain artefact. Finally, somewhere near the end, it is revealed that they are looking for valuable, but dangerous artefacts. The locations are presumed to lie hidden deep in Desmonds mind.