Assassin's Creed has always had fantastical stories, but it usually reins in its bizarre choices for "safe" endings. However, sometimes, a creative choice goes through that makes fans go "what the hell?". Of course, it's to be expected with the franchise's increasingly fantastical shift in tone.
That said, the weirdness had to start somewhere. These narrative twists and reveals throughout the franchise show that the franchise's writers tend to write by the seat of their pants. Whether good or bad, what's true is that these reveal caused a lot of discussions.
Aya Was The Hero, Not Bayek
Assassin's Creed: Origins was the most outwardly different game from its predecessors, for better or for worse. Gone are the elaborate robes and stealth segments (mostly), and in are the fantastical elements and RPG combat. The story as well has changed drastically in tone.
As u/Jobr95 succinctly put "Aya's part at the end felt very forced. The whole game has you playing as Bayek so you expect that he will be the leader at the end and get an epic finale, then suddenly it switches to Aya and she does everything and gets to be the mentor." Instead of a satisfying ending, players get an unearned "passing of the torch" for a torch that didn't need passing.
Élise de la Serre's Fate
Assassin's Creed Unity might have been best known for its buggy release than its French Revolution setting, but that doesn't make the story any less polarizing. Arno already had the issue of being rather bland, but at least players could latch onto Élise. Unfortunately, that wouldn't last. As u/Treshcore puts it:
"She was killed. Okay Ubisoft, so what did you want with that unexpected plot move? To make us cry? It's individual, but okay, let's pretend you did. Then what? Didn't you think that death is a scenery trope too, and you misuse it way too much?". This Redditor's points were well-reasoned. Elise was a far more fascinating character, and her death came off as nothing more than a cheap attempt to shock the player in an otherwise bland entry of the franchise.
Flavius Who?
Assassin's Creed: Origins was a breath of fresh air for the franchise, but it still suffered a lot in the narrative department. Apart from the ending, there was also the big reveal of Flavius as the villain. Most fans wouldn't blame anybody if they forgot that it was supposed to be a big reveal. Flavius isn't exactly one of the "best" characters in Origins.
As u/BlackFlash9 says about the character: "Flavius failed in making Bayek's destination feel anything worthwhile. There was hardly any satisfaction in killing him since I, and even Bayek to some degree barely knew him." The twist that he was the main villain was akin to Random Lioness from Background in The Lion King is the one who killed Mufasa, not Scar all along.
The Assassins Were Just As Bad (Apparently)
Assassin's Creed Rogue puts forth a genuinely interesting question: How far are the Assassins willing to go to fight against the Templars? This could lead to a slow burn for the character, as they realize just how similar they are to the Templars, only stopping short of true evil. Unfortunately, the game throws all that out of the window by revealing some Assassins were super evil all along.
In a comment, u/Saixak says this: "That whole game was a Shakespearean tragedy. If anyone decided to sit down and have an honest conversation, then it would have all been resolved. But because the plot needed it, everyone dropped a few IQ points and the Assassins became as merciless for no good reason." Add the ridiculous last-minute twist that Shay joins the Templars because "the Assassins kill innocents", only to follow it with Shay's controversial next target, and the game flounders as a result.
Odyssey's Odd DLC
Odyssey was praised for a "return to form" of main characters after dealing with stoic warrior types for a few games. Now, Alexandros and Kassandra have the choice to be snarky, irreverent rebels like Ezio was in the early games. Both assassins even get to be in same-sex romances, some of which last into the ending. Then all of a sudden, as u/PersonMcHuman summarizes: "The game’s second DLC forces your character into a straight relationship because of family and love, no matter if you were playing the game as an extremely gay murder-hobo. "
For people who chose that path, it makes sense, but for those who went their way, this was a slap in the face. Not to mention, having both characters pick the "straight" option canonically and the achievement is called "Growing Up" is its can of worms.
Shay's Ties to Unity
Rogue already had a bit of a controversial plot, but its ending took most of the attention. There, it is revealed that Shay was the person responsible for murdering Arno's father and kickstarting the entire plot of Unity. One would think such a reveal would have massive implications for the rest of the series.
But nothing ever came of it. Something that didn't miss u/RKO-Cutter's attention: "Nah, the worst part is we never hear of Shay again, just a vague statement that he lived the rest of his days as a Templar. I was expecting Arno to confront him at some point (I played Rogue before Unity) but nothing happened". The twist itself was solid, but unfortunately, it didn't amount to anything. Both Arno and Shay were shuffled off to the annals of the AC wiki, a fun fact to be read instead of an ending to be enjoyed.
Ratonhnhaké:ton's Fate
After everything that Ratonhnhaké:ton goes through, it's revealed that he was simply a cog all along. The player is forced to listen to a magical woman vaguely discuss prophecies, before Ratonhnhaké:ton is promptly shooed away, having done "his part" in history. Though not fond of the character, u/jackedup388 does feel for his unfortunate role:
"The treatment he gets by the isu is so disrespectful, it pissed me off. It's the same treatment they gave my powerful boy Ezio at the end of 2! "You've done your part for Desmond, now buzz off!" Holy hell I hate these ancient beings." Thankfully, the rest of his ending is surprisingly bittersweet. After all, it's not like fans of the series aren't used to non-Desmond MCs being disrespected by the Isu.
The Fake Apple(?) of Eden
The Apples of Eden are the most important magical plot devices of the franchise. All the characters seek it out for their ends, and it often leads to "disagreements". Revelations was an entire game dedicated to both the Templars and Assassins chasing a piece of Eden. Unfortunately, it was all for naught, as a Redditor explains:
"The part I didn't like about the ending was that the apple/treasure that Templars were searching for ended up being pointless. That apple eventually ended up in the hands of Queen Elizabeth.... and then who knows. The only one that matters is the one that Desmond currently has, which is the first one that Altair retrieved and then brought to Cyprus." In short, it was a glorified game of Telephone, with Ezio passing along a vague message to Desmond that ultimately amounts to nothing.
Desmond's Fate
Desmond, alongside Ezio, is the most familiar character for fans of the first five games in the franchise. It was his story in the modern day that glued all of the Assassin plots together. In not at all subtle ways, the narrative was building him up to be "The Savior" character. As u/jackedup388 says once more, however:
"Back in the future with Desmond, we got 2 of these [very rude words] arguing and literally just info dumping for the last 10 minutes of the game. Some prophecy about desmond is revealed and then he sacked himself to save the world and freed one of them. And then... NOTHING!". Desmond dies as two holograms argue over his corpse. A whimper of an end for a character built up across five games. At least players get to control an Abstergo QA tester in the future, which patently not the same.
Juno's Fate (In The Comics)
The entire crux of the pre-Origins Assassin's Creed games was the reveal that Juno, an ancient being, was responsible for both the Apples and pretty much everything that happens in the franchise. Not only that, Juno is Desmond's final adversary in the modern day. Desmond's character arc was sacrificed to prop up this major villain.
So imagine the player's shock after this reveal from u/TheBaconsRebellion's comment: "Ubisoft killed Juno off in a comic." It's as disappointing as players think that statement sounds. It's the video game equivalent of ending Return of the Jedi with Luke dying, and Palpatine at large, only for him to get unceremoniously killed off in a random episode of Star Wars: Rebels.