Symbology In Assassin's Creed
I figured I'd try to explain the deeper meaning behind the story.
Sofia in this film represents Sophia of Gnosticism. After Callum dies he wakes up in Sophia's care. This is not coincidental. Sophia is "the judge, the Virgin of Light" that either opens for a soul or closes against them in the light realm.
Callum may be a combination of Thomas from the Hymn of the Pearl as well as the gnostic Jesus. Let's start with Thomas. In the Hymn of the Pearl he is sent to retrieve a pearl from a serpent. Along the way he is seduced into forgetting who he is, his mission, and his family. His father sends him a message that reminds him of his past which allows him to recall his life and bring back the pearl.
The Animus in this case is the letter that contains his origins. Callum forgets his past life until the Animus reveals it to him. Another aspect of the Hymn of the Pearl is that in the end he puts back on his "glorious garment". Just as Callum puts on the assassin's clothes which his ancestor had worn. And of course Callum gets the "pearl" or Apple of Eden.
Sophia and Jesus are more complicated. As far as I understand, Sophia tries to emanate (give birth) without her consort Christ. The result is a fall from grace that creates a flawed material world where she exists longing for a return to the fullness of light or divinity. Although the world she has produced is imperfect, Sophia being the goddess, left it with sparks of light which are knowledge and goodness.
In other words, the Animus is the divine light (or knowledge) of Sophia which enables Callum and the other assassins to understand the truth of reality. It helps them become strong and reclaim their ancestry which is both from Sophia and in essence is Sophia. That is partly why Callum had no desire to hurt her.
Why do I say Callum is Jesus? For starters, his name means dove which is connected to Jesus and Sophia. The main reason though is that he is the last descendant who can retrieve the Apple of Eden and thereby save Sophia and the world. His singular potential makes his identity clear.
Who are the Templars meant to be? For the mythology of this film they signify the Archon who hold Sophia captive. She does not understand their intentions at first. Most likely as a result of her light, or knowledge, being taken from her. They pressure her to use the Animus for their gain. "Save me then now, O Light, for I lacked my light, which they have taken away, and I needed my power, which they have taken from me."
At the end Sophia appears to still be in darkness. She is not ready to join with Callum and, using the Apple of Eden, bring wholeness to the world. It is only by the unity of the divine feminine and divine masculine that good can permanently triumph over evil in Gnosticism. Christ and Sophia have an equal need for each other. The future consummation of their love, the combining of their light, is meant to bring healing except of course for the darkness which it will obliterate, it will "be like something that never was."