Ok, so this playthrough has some major plot secrets in it. After the first memory in sequence one, you can wear assassins outfits despite the fact that the customization menu has not been unlocked for the memory being played, and Arno hasn't gained assassin robes yet. So sequence1 memory 2 you're suppose to wear Altait's outfit (I used the Thomas outfit as a substitute), sequence 1 memory 3, Ezio's robes. next memory Connor, next memory Edward, next memory Shay.
What's the meaning of this? Well If you pay attention to the story, the story in each memory seems to adapt to the outfit worn, most notably during the Connor/Edward sequences. Connor's memory starts with him going into prison, and develops as Bellec tell you that your "father" fought for "Liberty". There's also a joke within the prison where one of the other prisoner is screaming that "they're killing everyone in here!" when in fact everyone is safe, but if you're replaying the memory, you can equip the pistol or phantom blades and kill the guards outside the prison cells. at the end of Connor's sequence you are on a rooftop drinking alcohol. Next sequence is Edward, this memory usually starts with you locating the assassin's guild and a lengthy cutscene where you meet the assassins council and proceed to have a psychedelic trip where you watch an assassin kill your father, then you proceed to chase the assassin and kill him. When replaying this memory, it starts directly with Arno (in this case, dressed as Edward) confused, and then proceeding the memory as usual, chasing down a assassin, and killing him, just like the beginning of Assassin's Creed 4, mind you. In the first memory it is also worth while to mention that the sword you obtain at the end of the game "The sword of Eden" can be used. The sword had powers similar to the Apples of Eden until Arno killed the templar who wielded it.
So what does this actually mean? Well what it actually means is that after the events of Assassin's Creed 1 Warren Vidic put Desmond in a coma to continue his genetic research without receiving interference from Desmond and the entire story of Lucy helping Desmond escape from Abstergo was fabricated to make Desmond more willing to co-operate with the genetic research while he is trapped in his subconscious. But somehow I imagine a lot of people reading this won't believe me and will continue to believe that Desmond actually did escape from Abstergo and he actually found a magical Apple that let him control peoples minds and used it to return to Abstergo and kill Warren Vidic before he found more Magical Brains uhh,,, I mean Apples that would help him take over the world. He then proceeded to die when I magical entity from Nowhere Appeared and told him a story about the past and future that didn't make any sense whatsoever and then Desmond died due to mysterious circumstances that were never explained.
According to my alternative universe, where you're still technically Desmond, now trapped in the Animus, during the course of Brotherhood/Revelations, Lucy managed to get Warren Vidic arrested after he induced the coma, and now there is a tech team working with Desmond within the Animus to try to help him wake up. This part of my theory is based off incredibly vague things such as these magically things called "Helix Rifts" that appear in Assassin's Creed Unity where you have to collect data in order to rescue a assassin who is "trapped" in Abstergos Animus Servers. Sounds erie right?
It's also worth-while to mention that Altair's era of Assassins is the only group of assassins that have a actual real life background and was fairly well grounded in reality until that little artifact that you recovered in the beginning of the game turned out to be a magical artifact that can control peoples minds at the end of the game and how when Desmond steps out of the Animus for the final time there is a bunch of mysterious markings everyone including the phrase "I stepped into the abyss and never came back" indicating that, oh I don't know, maybe Desmond was actually trapped in the animus after that final sequence and he was only dreaming that he got out.
Idk.
https://youtu.be/j2C9KQTOKcs
https://youtu.be/NwEi6p2CFCM
https://youtu.be/V7Qud4sUhhE
https://youtu.be/yjg4FW5t3gY
https://youtu.be/PB2S_KI--Hw
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That game is garbage