I understand the basic plot but have a few questions:
How does the Animus machine work?
How did finding Callum enable the Animus to better able access ancient events?
Why did they need Callum to find the Apple of Eden when they have access to the actual events? In other words, isn't Callum just going to do whatever happened? This might be a dumb question as the Apple of Eden is about the unlocking of Free Will.
How does the Apple of Eden work?
The Animus works as a "reading" device of a person´s DNA, the games establishing DNA as a library of the experiences of one´s ancestors until their offspring is conceived -making the "genetic memory" to pass on to the new carrier. The machine syncronizes the actual person with the ancestor in a particular moment the latter lived, allowing whoever is operating the machine to see a live recreation of those moments. If the synching is good, whatever you see in the Animus is what exactly happened to that ancestor, having a 100% reliable view into the past.
Callum was a perfect subject for the Animus because he´s the only living descendant of Aguilar de Nerja, the Assassin the guys at Abstergo were after.
They do not have access to the actual events until they see them in the Animus, hence them needing Callum´s contribution. They do not know where the Apple is until they see it in the final regression (the scene with Columbus). It has nothing to do with free will.
The Apple of Eden was a device used by an ancient civilization -the Isu- to enslave humans, a lower race also populating Earth thousands of years ago. It´s not specified how it works exactly, but it was designed to influence on human minds, allowing the Isu to control them. Later on, the Templars would try the same thing, while the Assassin´s fighting them in order to defend mankind´s free will over order.