Haruka did make it all up just to confuse Ayato
- In the second episode, Haruka is explaining to Ayato that he's been brought out of Tokyo-Jupiter, and that the entire world he'd lived in was a lie and brainwashing. "That's what you've been taught, but as you can see, this place still exists. Hard to believe? Consider it an object lesson in not believing everything you're told. You're not a child, after all. In fact, for all you know, I might have contrived all of this just to confuse you some more... Of course, I wouldn't talk this way if I meant to deceive you, would I?"
- After playing through Assassin's Creed II we learn that there was a more advanced precursor race that had created humans in their image. Eventually they came to conflict and the precursors were wiped out while a calamity shook the world. This roughly matches up with when Bahbem tested his artificial god system, the RahXephon, and split the world along human and Mu lines.
- The Pieces of Eden are actually Mulian technology that got left behind when the worlds were split. The Mulian mind control and illusions through out Tokyo Jupiter are powered by Al-Mualim's Piece of Eden, or tech derived from it.
- Bahbem himself created the Templars. Most likely to serve three purposes. 1)To influence the world around him, 2)To find the Pieces of Eden and 3)Because he got bored waiting thousands of years for 2012 to roll along.
- The Animus itself is also based on Mulian technology, most likely derived from whatever Bahbem used to transfer his mind into his clones.
- By extension we can infer that Bahbem's process of transferring into clones is at least partially based on manipulating the Genetic Memory.
- The reason Abstergo and the Templars are trying to kick off their Instrumentality plot in late 2012 is to get the world ready for the end of The Age of Katun. Bahbem would like to remove as many interferences as possible from his plans and directing most of humanity according to his whims goes a long way toward that. When things didn't go as planned Bahbem decided to scrap the idea and launch his Mu invasion plan instead.
- Futagami is an Assassin himself, who decided to infiltrate the Earth Defense Federation and then TERRA to find out the truth of the Mulian war. His assassination of Bahbem was merely the final act in the millennia old feud between the Templars and the Assassins.
Dagor Dagorath, the apocalyptic 'Battle of Battles' in Tolkien's mythology, is also known as the Second Singing. This corresponds to the use of the Rahxephon to tune the world at the end of the series. In addition, the Mulians may either be descended from elves who left for the Grey Havens or the remnants of Númenor.