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-AC 1-3: Desmond's story. You said you know this, so I won't go into it. I think Juno being released was a side-effect of whatever Desmond did to save the world from the solar flare, but don't quote me on that.
AC 4: You're correct on this one. The player character is an Abstergo Entertainment employee, completely unconnected to the Assassin-Templar war at first, who happens to be particularly gifted when it comes to controlling an Animus. (It's implied in Rogue's present-day sections that only people with high concentrations of First Civilization DNA can pilot the memories of others this well.) Black Flag introduces the Sage, a First Civ geneticist who was Juno's lover Aita in life, and ultimately became semi-immortal by being reduced to sets of "junk DNA" in the human genome that basically rewrite unborn humans into clones of himself whenever their DNA lines up in the right way. The Abstergo IT guy, who is the current active form of the Sage (there can be more than one at a time), recognizes that your skill with the Animus makes you a prime candidate for Juno's consciousness (which he had you unknowingly install into AE's server bank) to take over your body. He sticks you with a non-lethal dosage of something to weaken your physical body enough for Juno to reach into your mind and overwrite you, but Abstergo guards bust in and kill him before he can start the process. The weird manifesto pieces you can find on sticky notes throughout AE's offices were written by John as the primary document of a cult called The Instruments of the First Will, a cell of double-agents opposed to both the Assassins and the Templars, whose goal is to revive the First Civ starting with Juno. The Instruments are a minor plot point in Black Flag, but they become increasingly more prevalent later on. The player character is put in charge of the Edward Kenway project at AE, presumably cracking open the rest of AE's secrets and full-synching with Kenway at some point; according to Ubisoft, their ultimate fate is up to you. By the time Rogue occurs, they've left the company.
Rogue: The present-day stuff is very similar to 4's, but without the Assassins or John to steer the new researcher/player character, they are eventually forced to join the Templars. Abstergo Entertainment has now released a scaled-down version of the Animus as a VR game console called the Helix.
Unity: There is a little modern-day stuff in this game, but after 4 and Rogue's segments were received so poorly, it's been reduced to non-playable set dressing. The intro establishes that you're a person playing a Templar memory sequence on their Helix, when a heretofore-unknown woman calling herself "Bishop" essentially inducts you into the Assassin Brotherhood as an "Initiate" (one of many) and gives you the rest of Arno Dorian's genetic memory to play through. Your goal is to find another Sage in Dorian's life to ensure that the Templars, who are now trying to sequence the First Civilization peoples' genome for unknown reasons, have as little access to past and present Sages as possible. Bishop's own goals and origins are completely shrouded in mystery; even Desmond's dad, currently the closest thing the Assassins have to a leader, basically let her take over the Initiate project because she asked to, and refuses to elaborate further.
Going into Syndicate: Again, you're an Initiate with a Helix who is being guided through a genetic memory sequence by Bishop. She implies that this isn't your first time doing so. You might or might not be the exact same Initiate from Unity; like the researcher in 4, Ubisoft says you can make of that what you will.
That's everything leading up to the intro cutscene of Syndicate as far as I remember.
This is such a great response, thank you so much for taking the time to write all that. This helps a lot!
Does the present day story becomes more important again in Origin and Odyssey? I really hope so as it was what binded all AC games together....