Okay, so, the black and white view of the Assassin's Creed plot is unreasonable. The Templars are not pure evil, and the Assassins are not pure good, existing only to stop the Templar Plan. So what do we know?
To start: the Assassins murder people. Call it selective murder, targeted killing, assassination, elimination; euphemisms for the the same thing.
Second, the Assassins proclaim to work in the dark to serve the light. They also proclaim that they wish to have no hand in the way people live their lives; as Ezio said, "Do not follow me, or anyone else."
It is a severely deluded mind that can rampage across nations murdering people while claiming to take a hands-off approach to social guidance. There is nothing more hands-on than murder.
We can assume, then, that the narrative given by our Assassin protagonists is false, deluded. We have unreliable narrators. Of course they will declare that their actions are justified. The Templars do the same. So we must assume that the Assassins are hiding something, or at the very least, that they are subconsciously acting contrary to their professed goals.
Evidence from the game suggests that the Assassins are no more than another mystical ritualistic secret society seeking power. There is plenty of evidence to support this. Assassin's Creed: Brotherhood's single player directly involves the development of the Assassin's social, economic, and military infrastructure. Look at each of the factions of the game:
- Courtesans: spy network, revenue generation
- Thieves: spy network, low-profile courier network, "revenue generation"
- Mercenaries: militia / reserve army
- Assassins: shadowy hit teams, interrogation
- Ezio (as a representative of the Brotherhood): economic micromanagement, favors granted to loyal tradesmen
The role of the player fits perfectly into this as well. Empower the player to slaughter everyone, and the player slaughters wantonly. This is a direct reflection of the way that the power accruing in the hands of the Assassins has corrupted the Assassin order.
Where does that leave the Templars? They too are a secret society vying for power, and the links between the Templars and the Assassins have already been established within the canon of the games: Al Mualim of Masyaf betrayed Altair in revealing that he too was a Templar. Later it is revealed that Altair beds with a Templar agent, Maria. It is not difficult to imagine that further infiltrations, alliances, and secret meetings took place between the two groups.
We also know that the Templar knighthood is fractured and self-destructive, since Al Mualim ordered Altair to kill off his nine brothers in knighthood, so it's also unreasonable to assume that the Assassins are the only secret society the Templars have to fear; they must also fear other branches and splinter groups of Templars. We also have to question the integrity of the Assassin order, and the possibility for conflicting groups therein. For one thing, we learn over the course of Ezio's travels in Italy that the Assassins have allies they may not always count on. Does this mean that there could be other, autonomous Assassin brotherhoods around?
In conclusion, not only is it impossible that the Assassin vs Templar conflict is such a simple battle of good vs evil, it's impossible that the conflict is limited to those two groups. The real conflict might be between dozens of secret societies scattered across the world, each vying for power (be it super sci-fi Piece of Eden or otherwise), and our narrators are too unreliable to tell it to us straight.
