Given that this is the long-awaited conclusion to the Desmond story arc, it is inevitable that tears will be shed.
* [[spoiler:Watching five-year-old Connor fail to save his mother from his burning village has to be one of '''the''' most heartbreaking moments in the entire franchise. In a franchise full of [[TearJerker Tear Jerkers]], that's really saying something.]]
** The kicker? [[spoiler:There is a Quick-Time Event to lift the logs trapping Kaniehti:io. No matter how quickly you mash the buttons, [[PlayerPunch she'll still perish.]]]]
*** Worse still, [[spoiler:it initially feels like she might have been saved if the man who entered had helped Connor instead of pulling him away... but given how quickly the roof caves in shortly thereafter, it only drives home that there was no hope of saving her.]]
** There's also [[spoiler:Kaniehti:io]]'s reaction. [[spoiler:Despite being trapped under debris in a burning longhouse, she calmly accepts her impending death and spends her final moments comforting her distraught son and affirming her love for him. Not only is this tragic in and of itself, but it can easily remind some players of [[WesternAnimation/TheLandBeforeTime Littlefoot's mom]].]]
* The strained father-son relationships, both in the past and present stories.
** Connor really resents Haytham not just for [[spoiler: being the leader of the Templars,]] but from how his father never made much of a presence in his early life. Also, while Haytham [[spoiler: recognizes Connor as an enemy,]] you still see him ''desperately'' trying to create some sort of connection with his son, only for Connor to rebuke his efforts.
*** Even worse when you realize that Connor himself [[spoiler: tried his best to avoid killing Haytham too. Despite being pretty cold to Haytham, he really wanted the idea of Templars joining hands with Assassins to come true.]] If only Haytham could have dropped his jerkass attitude and let [[spoiler:Charles Lee die...]]
*** After Connor finds his father's diary, it's a bitter reality dawning.
---> [[spoiler: '''Connor:''' I never knew him. Not really. I thought I had, but it wasn't until I read his journal that I realized I hadn't really known him at all. And it's too late now. Too late to tell him I misjudged him. Too late to tell him I'm sorry.]]
*** [[http://www.youtube.com/watch?v=tlau_HEnaYA Haytham's final journal entry]], as read aloud by Adrian Hough himself.
** Desmond and William don't have it much better either. Watching Desmond call out his father for using his son as an UnwittingPawn and concluding that Bill himself [[NotSoDifferent is just as bad as]] [[KnightTemplar the Templars]] is just painful to watch.
*** Late in the game, William departs alone to Cairo to get a power source. [[spoiler: Unsurprisingly, he gets captured. Surprisingly, when he's cornered by Templars in a museum, with minutes before they kill or capture him, he sends what he thinks is his final email to his son, apologizing fo everything mean he's done, hopes Desmond could someday forgive him, and reaffirms his love for his son]]. It's touching, but [[Heartwarming/AssassinsCreedIII heartwarming]] when [[spoiler: you rescue him. Singlehandedly]].
* Unlike other instalments, a lot of the Templars you have to kill are [[WellIntentionedExtremist well-intentioned extremists]] who genuinely want to save human lives. This makes the action of killing them more emotionally intense.
** [[spoiler:John Pitcairn. He knows that a war would result in colonists getting killed and thus was trying his best to parley and prevent a Revolutionary War from being triggered. Killing him didn't just stop the Templars, it also signed the death sentence for many fellow colonists and soldiers.]]
** [[spoiler:William Johnson. He is convinced that the currently amicable colonists would turn on the Natives once they were finished with the British, hence why he [[CruelToBeKind threatens the Mohawk chiefs to accept Templar control.]] Seeing him call Connor's naivety out is gut-wrenching, especially if you know [[DoomedByCanon what happens to the Natives once Americans began going West]].]]
** [[spoiler: Nicholas Biddle. Yes, he gained little something on the side and his methods were questionable, but his major goal was strenghtening the colonial navy, which is exactly what he accomplished. His codex entry mentions him being a good and fair leader to his crew. And like a good captain, he wanted to go down with the Randolph.]]
** [[spoiler: Even Benjamin Church, although a special kind of bastard who betrayed both Colonists and Templars, earns himself some plus points in the end by calling out Connor's naivety.]]
** [[spoiler: Hell even Thomas Hickey manages to get a touching death when he flat out admits to only caring about money and being a total hedonist because he doesn't see anything else worth living for, but he at least views himself as being better than Connor because he can actually have lots of money and women, while Connor will likely never achieve his dream of a world free of all evil and oppression.]]
** And, at the end of it all, [[spoiler: Charles Lee, who helped burn down your village and promise to take from you everything you held dear, has a bit of a poignant send off. First, there's the whole CorruptTheCutie angle, when you remember the earnest young man who aided Haytham before he began being corrupted. Then there's his death. Wounded by a gun shot from Connor, he goes to a tavern, and instead of an epic battle, calmly waits for his death, even offering Connor a drink before he kills him. The final death of the 6 templars carries very little satisfaction overall, because it is little more than final unfinished business rather than the completion of revenge. And for him to FaceDeathWithDignity like that was quite unexpected.]]
* The way Haytham states "Son" to Connor just as Connor disowned him as a father when he correctly assumed that he held onto the information that [[spoiler: Washington was the one who ordered the destruction of his village]] until it suited him. You can practically hear the MyGodWhatHaveIDone tone in that word.
* The death of [[spoiler: Achilles. Yes, he died peacefully of old age with a friend by his side but Connor just lost the last pillar of support in his life and the closest thing he ever had to a proper father figure.]]
* By the end of the game, Connor earns himself some major TheWoobie points. [[spoiler: Connor has literally lost everything and everyone important to him in his entire life fighting the Templars. His mother died when he was young, he's forced to kill his best friend over a misunderstanding, and his village up and leaves during the second epilogue. Achilles, the closest thing he had to a real father figure, dies and leaves him wondering if their war will ever truly end, and what he's going to do with his life if it ever does since he's been fighting for so long he doesn't know anything else. The nation he helped free is still seeped in oppression and nothing really changed in regards to the persecution of his people. To top it all off, he went through all of this simply to gain possession of a trinket that he's instructed to hide for a greater purpose by powers far beyond his imagining or understand, and like Altiar and Ezio before him, he'll probably never understand what the purpose and net result of all his suffering amounted to.]]
** The disbelief in his voice when he discovers the men whose ideals he was fighting for are almost equally as corrupt and selfish as those he opposed seals the deal. Both epilogue sequences, be it [[spoiler:chasing out the British oppressors while oppressing others]] or [[spoiler:seeing his village moved because the congress started to give away the native land to keep its own people quiet and content]]. Kudos to both animators and voice actor, because they both hammer home how much of a downer ending that really is for our hero.
** [[spoiler: The least saddest thing he had to do? Kill his own father.]]
* [[spoiler: It's a HeroicSacrifice, done to save the world, but the death of Desmond still qualifies. Five games we played as Desmond, and now he is gone, and it's quite possible that in saving the world and sacrificing himself, he's unleased something worse than the Templars.]]
** [[spoiler: So it's more like SenselessSacrifice instead...]]
*** [[spoiler: Not really. We may be fighting something worse than the Templars, but at least we'll be alive to fight.]]
** [[spoiler: The saddest thing for Desmond's ending? His fate could have been prevented. But when you realize Juno expertly manipulated several generations of your heroes to steer fate and history right up to a single point in time, where it would be the final choice "death of hundreds of millions" or "let me go free", giving herself a gun to hold against Desmond's (and whole world's) head, that is the real kicker of the bittersweet ending. Had Ziio not listened to her (who as the spirit guide of her tribe told her about Haytham's "lie") or had she failed to manipulate Connor to eradicate the Templars (both outcomes likely leading to the Vault being opened way before), or had the current day Assassins and Templars found their own solution instead of listening to hers and chasing their own tail, the ending might've been way happier indeed. Juno's final lie about the end being instant and painless is only a bitter cherry on the already poisoned cake.]]
* The game hints several times that [[spoiler:Lucy's death at the end of Brotherhood, possibly even the details of her alignment[[note]]although Vidic and Cross at least considered her loyal to ''them'', the closest to "''hard''" evidence is Lucy's letter to Clay... after all, the "reveal" of what Lucy's role in the prior games was? All in the form of a vision ''from Juno'' for Clay to see[[/note]] were little more than Juno's deception. Juno herself had admitted before that future is never given and there is more than enough space for debating whether the outcome she forced on Desmond to believe in was really all that likely to happen. Desmond's doubt on the issue is also pretty difficult to watch at times, not least since [[spoiler:he eventually denies William's attempt to tell him that his stabbing of Lucy was 'just' Juno's mind control, but when Desmond's claimed decision was made on possibly false claims by a BiggerBad with an agenda]]...
** And Desmond struggling with the messages from Juno and the First Civilization:
---> '''Desmond:''' I'm sick of all these fucking riddles! JUST TELL US WHAT YOU WANT!
* Achilles [[spoiler: was forced to live the remainder of his days on the Frontier while his fellow Assassins and students were hunted down by the Templars and executed. No wonder hes so cynical towards Connor, he was afraid he would suffer the same fate as the other Assassins.]]
* "Tyranny of King Washington" [[spoiler: kills off Connor's mom quite early when Washington takes her out with the Apple of Eden. After seeing how unreservedly ''happy'' Connor was to see his mother again, and not to mention desperately trying to get answers out of her about why his world has changed, to see him screaming "MOTHER!" and sprinting towards her dead body just makes the scene so much worse. At least as bad as watching her original death scene. [[KickTheDog Even in an alternate universe he can't hold on to her.]]]]
* Sam Adams [[spoiler: brutal death at the hands of Putnam in ''The Betrayal.'' And for a while it looks like Kanen'to:kon has died right along with him. Luckily, he survives.]]
** [[spoiler: Not for long, as he is shot by Bluecoats early on in "Redemption" while trying to kill Washington. To his credit, it takes something like six shots before he finally goes down.]]